|2013-10-11 10:35:09|# [ASSEMBLE] |2013-10-11 10:35:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.run |2013-10-11 10:35:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.run |2013-10-11 10:35:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.run |2013-10-11 10:35:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.run |2013-10-11 10:35:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.run |2013-10-11 10:35:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.run |2013-10-11 10:35:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.run |2013-10-11 10:35:19| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.run |2013-10-11 10:35:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.105.run |2013-10-11 10:35:21| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.run |2013-10-11 10:35:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.125.run |2013-10-11 10:35:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.run |2013-10-11 10:35:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.run |2013-10-11 10:35:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.run |2013-10-11 10:35:27| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.run |2013-10-11 10:35:28| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.run |2013-10-11 10:35:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.run |2013-10-11 10:35:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.run |2013-10-11 10:35:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.run |2013-10-11 10:35:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.run |2013-10-11 10:35:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.run |2013-10-11 10:35:34| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.run |2013-10-11 10:35:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.run |2013-10-11 10:35:36| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.run |2013-10-11 10:35:37| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.run |2013-10-11 10:35:38| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.run |2013-10-11 10:35:38| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.run |2013-10-11 10:35:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.run |2013-10-11 10:35:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.run |2013-10-11 10:35:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.run |2013-10-11 10:35:43| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.run |2013-10-11 10:35:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.run |2013-10-11 10:35:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.run |2013-10-11 10:35:46| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.run |2013-10-11 10:35:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.run |2013-10-11 10:35:49| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.run |2013-10-11 10:35:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.run |2013-10-11 10:35:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.run |2013-10-11 10:35:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.run |2013-10-11 10:35:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.run |2013-10-11 10:35:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.run |2013-10-11 10:35:54| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.105.run |2013-10-11 10:35:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.run |2013-10-11 10:35:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.125.run |2013-10-11 10:35:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.run |2013-10-11 10:35:58| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.run |2013-10-11 10:35:59| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.run |2013-10-11 10:36:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.run |2013-10-11 10:36:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.run |2013-10-11 10:36:04| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.run |2013-10-11 10:36:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.run |2013-10-11 10:36:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.run |2013-10-11 10:36:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.run |2013-10-11 10:36:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.run |2013-10-11 10:36:09| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.run |2013-10-11 10:36:09| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.run |2013-10-11 10:36:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.run |2013-10-11 10:36:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.run |2013-10-11 10:36:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.run |2013-10-11 10:36:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.run |2013-10-11 10:36:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.run |2013-10-11 10:36:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.run |2013-10-11 10:36:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.run |2013-10-11 10:36:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.run |2013-10-11 10:36:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.run |2013-10-11 10:36:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.run |2013-10-11 10:36:21| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.run |2013-10-11 10:36:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.run |2013-10-11 10:36:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.run |2013-10-11 10:36:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.run |2013-10-11 10:36:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.run |2013-10-11 10:36:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.run |2013-10-11 10:36:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.run |2013-10-11 10:36:27| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.run |2013-10-11 10:36:28| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.run |2013-10-11 10:36:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.run |2013-10-11 10:36:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.run |2013-10-11 10:36:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.run |2013-10-11 10:36:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.run |2013-10-11 10:36:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.run |2013-10-11 10:36:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.run |2013-10-11 10:36:34| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.run |2013-10-11 10:36:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.run |2013-10-11 10:36:36| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.run |2013-10-11 10:36:37| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.run |2013-10-11 10:36:38| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.run |2013-10-11 10:36:39| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.run |2013-10-11 10:36:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.125.run |2013-10-11 10:36:43| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.run |2013-10-11 10:36:44| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.run |2013-10-11 10:36:44| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.run |2013-10-11 10:36:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.run |2013-10-11 10:36:46| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.run |2013-10-11 10:36:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.run |2013-10-11 10:36:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.run |2013-10-11 10:36:49| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.run |2013-10-11 10:36:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.run |2013-10-11 10:36:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.run |2013-10-11 10:36:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.run |2013-10-11 10:36:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.run |2013-10-11 10:36:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.run |2013-10-11 10:36:54| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.run |2013-10-11 10:36:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.run |2013-10-11 10:36:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.run |2013-10-11 10:36:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.run |2013-10-11 10:36:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.run |2013-10-11 10:36:58| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.run |2013-10-11 10:36:59| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.run |2013-10-11 10:37:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.run |2013-10-11 10:37:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.run |2013-10-11 10:37:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.run |2013-10-11 10:37:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.run |2013-10-11 10:37:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.run |2013-10-11 10:37:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.run |2013-10-11 10:37:06| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.run |2013-10-11 10:37:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.run |2013-10-11 10:37:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.run |2013-10-11 10:37:09| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.run |2013-10-11 10:37:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.run |2013-10-11 10:37:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.run |2013-10-11 10:37:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.run |2013-10-11 10:37:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.run |2013-10-11 10:37:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.run |2013-10-11 10:37:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.run |2013-10-11 10:37:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.run |2013-10-11 10:37:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.run |2013-10-11 10:37:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.run |2013-10-11 10:37:19| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.run |2013-10-11 10:37:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.run |2013-10-11 10:37:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.run |2013-10-11 10:37:21| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.run |2013-10-11 10:37:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.run |2013-10-11 10:37:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.run |2013-10-11 10:37:25| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contigWIUPAC.fa |2013-10-11 10:37:25|# [ASSEMBLER] |2013-10-11 10:37:38| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig |2013-10-11 10:37:39| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.run |2013-10-11 10:37:40| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contigWIUPAC.fa |2013-10-11 10:37:44| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig |2013-10-11 10:37:44| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.run |2013-10-11 10:37:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contigWIUPAC.fa |2013-10-11 10:37:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig |2013-10-11 10:37:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.run |2013-10-11 10:37:49| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contigWIUPAC.fa |2013-10-11 10:37:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig |2013-10-11 10:37:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.run |2013-10-11 10:37:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contigWIUPAC.fa |2013-10-11 10:37:56| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig |2013-10-11 10:37:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.run |2013-10-11 10:37:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contigWIUPAC.fa |2013-10-11 10:38:00| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig |2013-10-11 10:38:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.run |2013-10-11 10:38:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contigWIUPAC.fa |2013-10-11 10:38:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig |2013-10-11 10:38:04| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.run |2013-10-11 10:38:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contigWIUPAC.fa |2013-10-11 10:38:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig |2013-10-11 10:38:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.run |2013-10-11 10:38:09| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contigWIUPAC.fa |2013-10-11 10:38:11| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig |2013-10-11 10:38:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.run |2013-10-11 10:38:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contigWIUPAC.fa |2013-10-11 10:38:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig |2013-10-11 10:38:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.run |2013-10-11 10:38:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contigWIUPAC.fa |2013-10-11 10:38:19| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig |2013-10-11 10:38:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.run |2013-10-11 10:38:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contigWIUPAC.fa |2013-10-11 10:38:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig |2013-10-11 10:38:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.run |2013-10-11 10:38:25| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contigWIUPAC.fa |2013-10-11 10:38:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig |2013-10-11 10:38:28| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.run |2013-10-11 10:38:30| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contigWIUPAC.fa |2013-10-11 10:38:33| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig |2013-10-11 10:38:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.run |2013-10-11 10:38:35| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contigWIUPAC.fa |2013-10-11 10:38:37| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig |2013-10-11 10:38:37| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.run |2013-10-11 10:38:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contigWIUPAC.fa |2013-10-11 10:38:41| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig |2013-10-11 10:38:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.run |2013-10-11 10:38:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contigWIUPAC.fa |2013-10-11 10:38:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig |2013-10-11 10:38:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.run |2013-10-11 10:38:47| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contigWIUPAC.fa |2013-10-11 10:38:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig |2013-10-11 10:38:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.run |2013-10-11 10:38:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contigWIUPAC.fa |2013-10-11 10:38:54| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig |2013-10-11 10:38:54| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.run |2013-10-11 10:38:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contigWIUPAC.fa |2013-10-11 10:38:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig |2013-10-11 10:38:58| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.run |2013-10-11 10:38:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contigWIUPAC.fa |2013-10-11 10:39:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig |2013-10-11 10:39:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.run |2013-10-11 10:39:03| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contigWIUPAC.fa |2013-10-11 10:39:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig |2013-10-11 10:39:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.run |2013-10-11 10:39:10| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contigWIUPAC.fa |2013-10-11 10:39:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig |2013-10-11 10:39:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.run |2013-10-11 10:39:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contigWIUPAC.fa |2013-10-11 10:39:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig |2013-10-11 10:39:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.run |2013-10-11 10:39:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contigWIUPAC.fa |2013-10-11 10:39:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig |2013-10-11 10:39:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.run |2013-10-11 10:39:31| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contigWIUPAC.fa |2013-10-11 10:39:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig |2013-10-11 10:39:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.run |2013-10-11 10:39:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contigWIUPAC.fa |2013-10-11 10:39:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig |2013-10-11 10:39:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.run |2013-10-11 10:39:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contigWIUPAC.fa |2013-10-11 10:39:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig |2013-10-11 10:39:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.run |2013-10-11 10:39:49| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contigWIUPAC.fa |2013-10-11 10:39:53| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig |2013-10-11 10:39:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.run |2013-10-11 10:39:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contigWIUPAC.fa |2013-10-11 10:39:59| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig |2013-10-11 10:39:59| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.run |2013-10-11 10:40:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contigWIUPAC.fa |2013-10-11 10:40:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig |2013-10-11 10:40:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.run |2013-10-11 10:40:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contigWIUPAC.fa |2013-10-11 10:40:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig |2013-10-11 10:40:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.run |2013-10-11 10:40:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.125.asm.contig |2013-10-11 10:40:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.125.run |2013-10-11 10:40:14| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.125.failed |2013-10-11 10:40:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contigWIUPAC.fa |2013-10-11 10:40:19| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig |2013-10-11 10:40:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.run |2013-10-11 10:40:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contigWIUPAC.fa |2013-10-11 10:40:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig |2013-10-11 10:40:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.run |2013-10-11 10:40:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contigWIUPAC.fa |2013-10-11 10:40:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig |2013-10-11 10:40:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.run |2013-10-11 10:40:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contigWIUPAC.fa |2013-10-11 10:40:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig |2013-10-11 10:40:36| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.run |2013-10-11 10:40:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contigWIUPAC.fa |2013-10-11 10:40:41| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig |2013-10-11 10:40:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.run |2013-10-11 10:40:44| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contigWIUPAC.fa |2013-10-11 10:40:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig |2013-10-11 10:40:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.run |2013-10-11 10:40:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contigWIUPAC.fa |2013-10-11 10:40:54| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig |2013-10-11 10:40:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.run |2013-10-11 10:40:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contigWIUPAC.fa |2013-10-11 10:41:00| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig |2013-10-11 10:41:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.run |2013-10-11 10:41:03| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contigWIUPAC.fa |2013-10-11 10:41:06| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig |2013-10-11 10:41:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.run |2013-10-11 10:41:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contigWIUPAC.fa |2013-10-11 10:41:12| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig |2013-10-11 10:41:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.run |2013-10-11 10:41:14| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contigWIUPAC.fa |2013-10-11 10:41:17| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig |2013-10-11 10:41:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.run |2013-10-11 10:41:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contigWIUPAC.fa |2013-10-11 10:41:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig |2013-10-11 10:41:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.run |2013-10-11 10:41:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contigWIUPAC.fa |2013-10-11 10:41:30| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig |2013-10-11 10:41:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.run |2013-10-11 10:41:34| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contigWIUPAC.fa |2013-10-11 10:41:38| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig |2013-10-11 10:41:39| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.run |2013-10-11 10:41:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contigWIUPAC.fa |2013-10-11 10:41:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig |2013-10-11 10:41:46| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.run |2013-10-11 10:41:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contigWIUPAC.fa |2013-10-11 10:41:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig |2013-10-11 10:41:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.run |2013-10-11 10:41:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contigWIUPAC.fa |2013-10-11 10:41:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig |2013-10-11 10:41:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.run |2013-10-11 10:42:00| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contigWIUPAC.fa |2013-10-11 10:42:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig |2013-10-11 10:42:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.run |2013-10-11 10:42:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contigWIUPAC.fa |2013-10-11 10:42:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig |2013-10-11 10:42:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.run |2013-10-11 10:42:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contigWIUPAC.fa |2013-10-11 10:42:16| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig |2013-10-11 10:42:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.run |2013-10-11 10:42:19| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contigWIUPAC.fa |2013-10-11 10:42:23| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig |2013-10-11 10:42:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.run |2013-10-11 10:42:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contigWIUPAC.fa |2013-10-11 10:42:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig |2013-10-11 10:42:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.run |2013-10-11 10:42:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contigWIUPAC.fa |2013-10-11 10:42:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig |2013-10-11 10:42:36| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.run |2013-10-11 10:42:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contigWIUPAC.fa |2013-10-11 10:42:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig |2013-10-11 10:42:44| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.run |2013-10-11 10:42:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contigWIUPAC.fa |2013-10-11 10:42:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig |2013-10-11 10:42:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.run |2013-10-11 10:42:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contigWIUPAC.fa |2013-10-11 10:42:56| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig |2013-10-11 10:42:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.run |2013-10-11 10:42:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contigWIUPAC.fa |2013-10-11 10:43:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig |2013-10-11 10:43:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.run |2013-10-11 10:43:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contigWIUPAC.fa |2013-10-11 10:43:09| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig |2013-10-11 10:43:09| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.run |2013-10-11 10:43:12| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contigWIUPAC.fa |2013-10-11 10:43:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig |2013-10-11 10:43:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.run |2013-10-11 10:43:19| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contigWIUPAC.fa |2013-10-11 10:43:22| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig |2013-10-11 10:43:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.run |2013-10-11 10:43:25| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contigWIUPAC.fa |2013-10-11 10:43:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig |2013-10-11 10:43:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.run |2013-10-11 10:43:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.105.asm.contig |2013-10-11 10:43:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.105.run |2013-10-11 10:43:31| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.105.failed |2013-10-11 10:43:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.125.asm.contig |2013-10-11 10:43:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.125.run |2013-10-11 10:43:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.125.failed |2013-10-11 10:43:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contigWIUPAC.fa |2013-10-11 10:43:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig |2013-10-11 10:43:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.run |2013-10-11 10:43:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contigWIUPAC.fa |2013-10-11 10:43:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig |2013-10-11 10:43:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.run |2013-10-11 10:43:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contigWIUPAC.fa |2013-10-11 10:43:52| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig |2013-10-11 10:43:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.run |2013-10-11 10:43:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contigWIUPAC.fa |2013-10-11 10:44:00| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig |2013-10-11 10:44:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.run |2013-10-11 10:44:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contigWIUPAC.fa |2013-10-11 10:44:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig |2013-10-11 10:44:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.run |2013-10-11 10:44:10| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contigWIUPAC.fa |2013-10-11 10:44:13| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig |2013-10-11 10:44:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.run |2013-10-11 10:44:18| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contigWIUPAC.fa |2013-10-11 10:44:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig |2013-10-11 10:44:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.run |2013-10-11 10:44:25| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contigWIUPAC.fa |2013-10-11 10:44:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig |2013-10-11 10:44:28| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.run |2013-10-11 10:44:31| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contigWIUPAC.fa |2013-10-11 10:44:34| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig |2013-10-11 10:44:34| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.run |2013-10-11 10:44:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contigWIUPAC.fa |2013-10-11 10:44:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig |2013-10-11 10:44:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.run |2013-10-11 10:44:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contigWIUPAC.fa |2013-10-11 10:44:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig |2013-10-11 10:44:46| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.run |2013-10-11 10:44:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contigWIUPAC.fa |2013-10-11 10:44:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig |2013-10-11 10:44:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.run |2013-10-11 10:44:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contigWIUPAC.fa |2013-10-11 10:44:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig |2013-10-11 10:44:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.run |2013-10-11 10:44:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contigWIUPAC.fa |2013-10-11 10:45:01| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig |2013-10-11 10:45:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.run |2013-10-11 10:45:03| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contigWIUPAC.fa |2013-10-11 10:45:06| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig |2013-10-11 10:45:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.run |2013-10-11 10:45:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contigWIUPAC.fa |2013-10-11 10:45:11| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig |2013-10-11 10:45:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.run |2013-10-11 10:45:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contigWIUPAC.fa |2013-10-11 10:45:16| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig |2013-10-11 10:45:17| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.run |2013-10-11 10:45:19| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contigWIUPAC.fa |2013-10-11 10:45:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig |2013-10-11 10:45:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.run |2013-10-11 10:45:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contigWIUPAC.fa |2013-10-11 10:45:26| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig |2013-10-11 10:45:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.run |2013-10-11 10:45:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contigWIUPAC.fa |2013-10-11 10:45:31| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig |2013-10-11 10:45:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.run |2013-10-11 10:45:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contigWIUPAC.fa |2013-10-11 10:45:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig |2013-10-11 10:45:37| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.run |2013-10-11 10:45:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contigWIUPAC.fa |2013-10-11 10:45:41| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig |2013-10-11 10:45:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.run |2013-10-11 10:45:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contigWIUPAC.fa |2013-10-11 10:45:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig |2013-10-11 10:45:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.run |2013-10-11 10:45:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contigWIUPAC.fa |2013-10-11 10:45:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig |2013-10-11 10:45:51| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.run |2013-10-11 10:45:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contigWIUPAC.fa |2013-10-11 10:45:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig |2013-10-11 10:45:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.run |2013-10-11 10:45:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contigWIUPAC.fa |2013-10-11 10:46:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig |2013-10-11 10:46:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.run |2013-10-11 10:46:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contigWIUPAC.fa |2013-10-11 10:46:08| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig |2013-10-11 10:46:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.run |2013-10-11 10:46:10| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contigWIUPAC.fa |2013-10-11 10:46:13| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig |2013-10-11 10:46:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.run |2013-10-11 10:46:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contigWIUPAC.fa |2013-10-11 10:46:19| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig |2013-10-11 10:46:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.run |2013-10-11 10:46:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contigWIUPAC.fa |2013-10-11 10:46:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig |2013-10-11 10:46:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.run |2013-10-11 10:46:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contigWIUPAC.fa |2013-10-11 10:46:30| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig |2013-10-11 10:46:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.run |2013-10-11 10:46:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contigWIUPAC.fa |2013-10-11 10:46:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig |2013-10-11 10:46:36| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.run |2013-10-11 10:46:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contigWIUPAC.fa |2013-10-11 10:46:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig |2013-10-11 10:46:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.run |2013-10-11 10:46:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.asm.contigWIUPAC.fa |2013-10-11 10:47:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.asm.contig |2013-10-11 10:48:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.run |2013-10-11 10:48:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.asm.contigWIUPAC.fa |2013-10-11 10:48:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.asm.contig |2013-10-11 10:48:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.35.run |2013-10-11 10:48:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.asm.contigWIUPAC.fa |2013-10-11 10:49:26| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.asm.contig |2013-10-11 10:49:27| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.41.run |2013-10-11 10:49:29| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.asm.contigWIUPAC.fa |2013-10-11 10:50:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.asm.contig |2013-10-11 10:50:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.45.run |2013-10-11 10:50:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa |2013-10-11 10:50:34| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.asm.contig |2013-10-11 10:50:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.55.run |2013-10-11 10:50:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.asm.contigWIUPAC.fa |2013-10-11 10:50:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.asm.contig |2013-10-11 10:50:59| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.65.run |2013-10-11 10:51:00| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.asm.contigWIUPAC.fa |2013-10-11 10:51:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.asm.contig |2013-10-11 10:51:19| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.75.run |2013-10-11 10:51:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.asm.contigWIUPAC.fa |2013-10-11 10:51:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.asm.contig |2013-10-11 10:51:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.85.run |2013-10-11 10:51:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.asm.contigWIUPAC.fa |2013-10-11 10:51:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.asm.contig |2013-10-11 10:51:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.95.run |2013-10-11 10:51:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.asm.contigWIUPAC.fa |2013-10-11 10:51:34| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.asm.contig |2013-10-11 10:51:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.run |2013-10-11 10:51:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.asm.contigWIUPAC.fa |2013-10-11 10:51:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.asm.contig |2013-10-11 10:51:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.run |2013-10-11 10:51:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contigWIUPAC.fa |2013-10-11 10:51:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig |2013-10-11 10:51:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.run |2013-10-11 10:51:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contigWIUPAC.fa |2013-10-11 10:51:53| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig |2013-10-11 10:51:54| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.run |2013-10-11 10:51:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contigWIUPAC.fa |2013-10-11 10:51:59| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig |2013-10-11 10:52:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.run |2013-10-11 10:52:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contigWIUPAC.fa |2013-10-11 10:52:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig |2013-10-11 10:52:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.run |2013-10-11 10:52:06| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contigWIUPAC.fa |2013-10-11 10:52:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig |2013-10-11 10:52:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.run |2013-10-11 10:52:12| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contigWIUPAC.fa |2013-10-11 10:52:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig |2013-10-11 10:52:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.run |2013-10-11 10:52:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contigWIUPAC.fa |2013-10-11 10:52:20| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig |2013-10-11 10:52:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.run |2013-10-11 10:52:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contigWIUPAC.fa |2013-10-11 10:52:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig |2013-10-11 10:52:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.run |2013-10-11 10:52:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contigWIUPAC.fa |2013-10-11 10:52:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig |2013-10-11 10:52:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.run |2013-10-11 10:52:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.105.asm.contig |2013-10-11 10:52:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.105.run |2013-10-11 10:52:31| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.105.failed |2013-10-11 10:52:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.125.asm.contig |2013-10-11 10:52:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.125.run |2013-10-11 10:52:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.125.failed |2013-10-11 10:52:35| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contigWIUPAC.fa |2013-10-11 10:52:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig |2013-10-11 10:52:46| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.run |2013-10-11 10:52:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contigWIUPAC.fa |2013-10-11 10:52:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig |2013-10-11 10:52:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.run |2013-10-11 10:52:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contigWIUPAC.fa |2013-10-11 10:52:56| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig |2013-10-11 10:52:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.run |2013-10-11 10:52:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contigWIUPAC.fa |2013-10-11 10:53:01| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig |2013-10-11 10:53:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.run |2013-10-11 10:53:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contigWIUPAC.fa |2013-10-11 10:53:08| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig |2013-10-11 10:53:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.run |2013-10-11 10:53:11| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contigWIUPAC.fa |2013-10-11 10:53:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig |2013-10-11 10:53:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.run |2013-10-11 10:53:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contigWIUPAC.fa |2013-10-11 10:53:20| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig |2013-10-11 10:53:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.run |2013-10-11 10:53:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contigWIUPAC.fa |2013-10-11 10:53:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig |2013-10-11 10:53:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.run |2013-10-11 10:53:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contigWIUPAC.fa |2013-10-11 10:53:31| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig |2013-10-11 10:53:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.run |2013-10-11 10:53:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contigWIUPAC.fa |2013-10-11 10:53:37| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig |2013-10-11 10:53:38| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.run |2013-10-11 10:53:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contigWIUPAC.fa |2013-10-11 10:53:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig |2013-10-11 10:53:43| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.run |2013-10-11 10:53:44| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contigWIUPAC.fa |2013-10-11 10:53:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig |2013-10-11 10:53:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.run |2013-10-11 10:53:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contigWIUPAC.fa |2013-10-11 10:54:00| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig |2013-10-11 10:54:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.run |2013-10-11 10:54:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contigWIUPAC.fa |2013-10-11 10:54:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig |2013-10-11 10:54:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.run |2013-10-11 10:54:06| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contigWIUPAC.fa |2013-10-11 10:54:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig |2013-10-11 10:54:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.run |2013-10-11 10:54:11| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contigWIUPAC.fa |2013-10-11 10:54:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig |2013-10-11 10:54:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.run |2013-10-11 10:54:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contigWIUPAC.fa |2013-10-11 10:54:19| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig |2013-10-11 10:54:19| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.run |2013-10-11 10:54:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contigWIUPAC.fa |2013-10-11 10:54:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig |2013-10-11 10:54:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.run |2013-10-11 10:54:25| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contigWIUPAC.fa |2013-10-11 10:54:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig |2013-10-11 10:54:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.run |2013-10-11 10:54:30| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contigWIUPAC.fa |2013-10-11 10:54:33| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig |2013-10-11 10:54:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.run |2013-10-11 10:54:34| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contigWIUPAC.fa |2013-10-11 10:54:37| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig |2013-10-11 10:54:37| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.run |2013-10-11 10:54:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contigWIUPAC.fa |2013-10-11 10:54:42| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. RemoveIUPAC /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contigWIUPAC.fa >/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig |2013-10-11 10:54:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.run |2013-10-11 10:54:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.asm.contig |2013-10-11 10:54:43| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.run |2013-10-11 10:54:43| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.failed |2013-10-11 10:54:44| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/assemble.success |2013-10-11 10:54:51|# [MAPREADS] |2013-10-11 10:55:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 10:55:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 10:56:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.fasta.qual |2013-10-11 10:57:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.hdr |2013-10-11 10:57:23| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.mappedmates |2013-10-11 10:57:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 10:58:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 10:58:41| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.fasta.qual |2013-10-11 11:00:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.hdr |2013-10-11 11:00:06| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.mappedmates |2013-10-11 11:00:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:01:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:01:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.fasta.qual |2013-10-11 11:02:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.hdr |2013-10-11 11:02:48| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.mappedmates |2013-10-11 11:03:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:03:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:04:01| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.fasta.qual |2013-10-11 11:05:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.hdr |2013-10-11 11:05:30| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.mappedmates |2013-10-11 11:05:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:06:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:06:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.fasta.qual |2013-10-11 11:08:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.hdr |2013-10-11 11:08:09| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.mappedmates |2013-10-11 11:08:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:09:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:09:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.fasta.qual |2013-10-11 11:10:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.hdr |2013-10-11 11:10:52| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.mappedmates |2013-10-11 11:11:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:11:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:12:06| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.fasta.qual |2013-10-11 11:13:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.hdr |2013-10-11 11:13:33| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.mappedmates |2013-10-11 11:13:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:14:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:14:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.fasta.qual |2013-10-11 11:16:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.hdr |2013-10-11 11:16:16| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.mappedmates |2013-10-11 11:16:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:17:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:17:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.fasta.qual |2013-10-11 11:18:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.hdr |2013-10-11 11:18:59| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.mappedmates |2013-10-11 11:19:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:19:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:20:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.fasta.qual |2013-10-11 11:21:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.hdr |2013-10-11 11:21:47| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.mappedmates |2013-10-11 11:22:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:22:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:23:38| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.fasta.qual |2013-10-11 11:24:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.hdr |2013-10-11 11:24:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.mappedmates |2013-10-11 11:25:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:25:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:26:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.fasta.qual |2013-10-11 11:27:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.hdr |2013-10-11 11:27:47| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.mappedmates |2013-10-11 11:28:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:28:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:29:20| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.fasta.qual |2013-10-11 11:30:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.hdr |2013-10-11 11:30:43| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.mappedmates |2013-10-11 11:31:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:31:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:32:16| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.fasta.qual |2013-10-11 11:33:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.hdr |2013-10-11 11:33:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.mappedmates |2013-10-11 11:34:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:34:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:35:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.fasta.qual |2013-10-11 11:36:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.hdr |2013-10-11 11:36:33| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.mappedmates |2013-10-11 11:36:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:37:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:37:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.fasta.qual |2013-10-11 11:39:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.hdr |2013-10-11 11:39:21| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.mappedmates |2013-10-11 11:39:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:40:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:40:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.fasta.qual |2013-10-11 11:42:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.hdr |2013-10-11 11:42:07| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.mappedmates |2013-10-11 11:42:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:43:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:43:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.fasta.qual |2013-10-11 11:44:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.hdr |2013-10-11 11:44:56| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.mappedmates |2013-10-11 11:45:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:45:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:46:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.fasta.qual |2013-10-11 11:47:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.hdr |2013-10-11 11:47:42| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.mappedmates |2013-10-11 11:48:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:48:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:49:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.fasta.qual |2013-10-11 11:50:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.hdr |2013-10-11 11:50:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.mappedmates |2013-10-11 11:50:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:51:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:52:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.fasta.qual |2013-10-11 11:53:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.hdr |2013-10-11 11:53:23| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.mappedmates |2013-10-11 11:53:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:54:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:54:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.fasta.qual |2013-10-11 11:56:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.hdr |2013-10-11 11:56:11| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.mappedmates |2013-10-11 11:56:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:57:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 11:57:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.fasta.qual |2013-10-11 11:58:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.hdr |2013-10-11 11:59:00| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.mappedmates |2013-10-11 11:59:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 11:59:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:00:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.fasta.qual |2013-10-11 12:01:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.hdr |2013-10-11 12:01:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.mappedmates |2013-10-11 12:02:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:02:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:03:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.fasta.qual |2013-10-11 12:04:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.hdr |2013-10-11 12:04:29| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.mappedmates |2013-10-11 12:04:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:05:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:05:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.fasta.qual |2013-10-11 12:07:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.hdr |2013-10-11 12:07:21| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.mappedmates |2013-10-11 12:07:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:08:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:08:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.fasta.qual |2013-10-11 12:10:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.hdr |2013-10-11 12:10:18| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.mappedmates |2013-10-11 12:10:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:11:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:11:53| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.fasta.qual |2013-10-11 12:13:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.hdr |2013-10-11 12:13:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.mappedmates |2013-10-11 12:13:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:14:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:14:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.fasta.qual |2013-10-11 12:16:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.hdr |2013-10-11 12:16:05| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.mappedmates |2013-10-11 12:16:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:16:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:17:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta.qual |2013-10-11 12:18:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr |2013-10-11 12:18:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates |2013-10-11 12:19:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:19:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:20:11| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.fasta.qual |2013-10-11 12:21:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.hdr |2013-10-11 12:21:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.mappedmates |2013-10-11 12:22:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:22:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:23:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.fasta.qual |2013-10-11 12:24:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.hdr |2013-10-11 12:24:28| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.mappedmates |2013-10-11 12:24:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:25:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:25:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.fasta.qual |2013-10-11 12:27:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.hdr |2013-10-11 12:27:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.mappedmates |2013-10-11 12:27:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:28:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:28:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.fasta.qual |2013-10-11 12:30:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.hdr |2013-10-11 12:30:00| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.mappedmates |2013-10-11 12:30:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:30:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:31:12| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.fasta.qual |2013-10-11 12:32:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.hdr |2013-10-11 12:32:50| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.mappedmates |2013-10-11 12:33:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:33:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:34:04| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.fasta.qual |2013-10-11 12:35:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.hdr |2013-10-11 12:35:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.mappedmates |2013-10-11 12:36:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:36:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:36:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.fasta.qual |2013-10-11 12:38:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.hdr |2013-10-11 12:38:33| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.mappedmates |2013-10-11 12:38:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:39:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:39:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.fasta.qual |2013-10-11 12:41:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.hdr |2013-10-11 12:41:25| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.mappedmates |2013-10-11 12:41:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:42:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:42:37| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.fasta.qual |2013-10-11 12:44:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.hdr |2013-10-11 12:44:11| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.mappedmates |2013-10-11 12:44:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:45:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:45:31| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.fasta.qual |2013-10-11 12:47:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.hdr |2013-10-11 12:47:06| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.mappedmates |2013-10-11 12:47:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:48:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:48:22| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.fasta.qual |2013-10-11 12:50:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.hdr |2013-10-11 12:50:02| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.mappedmates |2013-10-11 12:50:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:50:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:51:42| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.fasta.qual |2013-10-11 12:53:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.hdr |2013-10-11 12:53:05| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.mappedmates |2013-10-11 12:53:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 12:53:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 12:55:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.fasta.qual |2013-10-11 12:56:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.hdr |2013-10-11 12:56:16| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.mappedmates |2013-10-11 12:58:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:00:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:01:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.fasta.qual |2013-10-11 13:02:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.hdr |2013-10-11 13:02:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.mappedmates |2013-10-11 13:03:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:04:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:04:27| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.fasta.qual |2013-10-11 13:06:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.hdr |2013-10-11 13:06:09| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.mappedmates |2013-10-11 13:06:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:07:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:07:27| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.fasta.qual |2013-10-11 13:09:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.hdr |2013-10-11 13:09:07| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.mappedmates |2013-10-11 13:09:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:10:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:10:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.fasta.qual |2013-10-11 13:12:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.hdr |2013-10-11 13:12:06| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.mappedmates |2013-10-11 13:12:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:13:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:13:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.fasta.qual |2013-10-11 13:14:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.hdr |2013-10-11 13:15:00| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.mappedmates |2013-10-11 13:15:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:15:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:16:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.fasta.qual |2013-10-11 13:17:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.hdr |2013-10-11 13:17:55| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.mappedmates |2013-10-11 13:18:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:18:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:19:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.fasta.qual |2013-10-11 13:20:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.hdr |2013-10-11 13:20:46| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.mappedmates |2013-10-11 13:21:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:21:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:22:08| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.fasta.qual |2013-10-11 13:23:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.hdr |2013-10-11 13:23:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.mappedmates |2013-10-11 13:23:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:24:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:25:06| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.fasta.qual |2013-10-11 13:26:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.hdr |2013-10-11 13:26:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.mappedmates |2013-10-11 13:26:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:27:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:28:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.fasta.qual |2013-10-11 13:29:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.hdr |2013-10-11 13:29:30| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.mappedmates |2013-10-11 13:29:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:30:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:31:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.fasta.qual |2013-10-11 13:32:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.hdr |2013-10-11 13:32:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.mappedmates |2013-10-11 13:32:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:33:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:34:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.fasta.qual |2013-10-11 13:35:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.hdr |2013-10-11 13:35:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.mappedmates |2013-10-11 13:36:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:36:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:37:17| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.fasta.qual |2013-10-11 13:38:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.hdr |2013-10-11 13:38:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.mappedmates |2013-10-11 13:39:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:39:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:40:13| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.fasta.qual |2013-10-11 13:41:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.hdr |2013-10-11 13:41:30| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.mappedmates |2013-10-11 13:41:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:42:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:43:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.fasta.qual |2013-10-11 13:44:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.hdr |2013-10-11 13:44:22| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.mappedmates |2013-10-11 13:44:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:45:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:45:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.fasta.qual |2013-10-11 13:47:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.hdr |2013-10-11 13:47:16| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.mappedmates |2013-10-11 13:47:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:48:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:48:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.fasta.qual |2013-10-11 13:50:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.hdr |2013-10-11 13:50:06| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.mappedmates |2013-10-11 13:50:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:51:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:51:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.fasta.qual |2013-10-11 13:52:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.hdr |2013-10-11 13:52:56| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.mappedmates |2013-10-11 13:53:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:54:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.fasta.qual |2013-10-11 13:55:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.hdr |2013-10-11 13:55:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.mappedmates |2013-10-11 13:56:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:56:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:57:23| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.fasta.qual |2013-10-11 13:58:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.hdr |2013-10-11 13:58:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.mappedmates |2013-10-11 13:58:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 13:59:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 13:59:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.unaligned.fasta.qual |2013-10-11 14:01:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.hdr |2013-10-11 14:01:25| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.105.lib1.mappedmates |2013-10-11 14:01:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 14:02:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 14:02:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.unaligned.fasta.qual |2013-10-11 14:04:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.hdr |2013-10-11 14:04:07| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.125.lib1.mappedmates |2013-10-11 14:13:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-11 14:31:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-11 14:33:20| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.unaligned.fasta.qual |2013-10-11 14:33:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.hdr |2013-10-11 14:33:50| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo.25.lib1.mappedmates |2013-10-14 12:51:59|# [MAPREADS] |2013-10-14 12:52:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 12:52:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 12:52:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.unaligned.fasta.qual |2013-10-14 12:54:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.hdr |2013-10-14 12:54:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.lib1.mappedmates |2013-10-14 12:54:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 12:55:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 12:55:26| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.unaligned.fasta.qual |2013-10-14 12:56:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.hdr |2013-10-14 12:56:51| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.lib1.mappedmates |2013-10-14 12:57:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 12:57:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 12:57:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.unaligned.fasta.qual |2013-10-14 12:59:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.hdr |2013-10-14 12:59:18| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.lib1.mappedmates |2013-10-14 12:59:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:00:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:00:27| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.unaligned.fasta.qual |2013-10-14 13:01:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.hdr |2013-10-14 13:01:48| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.lib1.mappedmates |2013-10-14 13:02:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:02:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:02:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.unaligned.fasta.qual |2013-10-14 13:04:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.hdr |2013-10-14 13:04:17| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.lib1.mappedmates |2013-10-14 13:04:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:05:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:05:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.unaligned.fasta.qual |2013-10-14 13:06:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.hdr |2013-10-14 13:06:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.lib1.mappedmates |2013-10-14 13:07:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:07:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:07:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.unaligned.fasta.qual |2013-10-14 13:09:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.hdr |2013-10-14 13:09:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.lib1.mappedmates |2013-10-14 13:09:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:10:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:10:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.unaligned.fasta.qual |2013-10-14 13:11:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.hdr |2013-10-14 13:11:47| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.lib1.mappedmates |2013-10-14 13:12:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:12:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:13:01| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.unaligned.fasta.qual |2013-10-14 13:14:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.hdr |2013-10-14 13:14:18| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.lib1.mappedmates |2013-10-14 13:14:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:15:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:15:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.unaligned.fasta.qual |2013-10-14 13:16:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.hdr |2013-10-14 13:16:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.lib1.mappedmates |2013-10-14 13:17:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:17:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:18:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.unaligned.fasta.qual |2013-10-14 13:19:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.hdr |2013-10-14 13:19:35| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.lib1.mappedmates |2013-10-14 13:19:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:20:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:21:09| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.unaligned.fasta.qual |2013-10-14 13:22:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.hdr |2013-10-14 13:22:19| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.lib1.mappedmates |2013-10-14 13:22:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:23:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:23:41| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.unaligned.fasta.qual |2013-10-14 13:24:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.hdr |2013-10-14 13:24:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.lib1.mappedmates |2013-10-14 13:25:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:25:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:26:19| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.unaligned.fasta.qual |2013-10-14 13:27:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.hdr |2013-10-14 13:27:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.lib1.mappedmates |2013-10-14 13:27:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:28:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:28:52| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.unaligned.fasta.qual |2013-10-14 13:30:11| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.hdr |2013-10-14 13:30:11| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.lib1.mappedmates |2013-10-14 13:30:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:31:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:31:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.unaligned.fasta.qual |2013-10-14 13:32:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.hdr |2013-10-14 13:32:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.lib1.mappedmates |2013-10-14 13:32:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:33:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:33:49| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.unaligned.fasta.qual |2013-10-14 13:35:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.hdr |2013-10-14 13:35:03| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.lib1.mappedmates |2013-10-14 13:35:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:35:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:36:13| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.unaligned.fasta.qual |2013-10-14 13:37:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.hdr |2013-10-14 13:37:28| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.lib1.mappedmates |2013-10-14 13:37:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:38:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:38:40| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.unaligned.fasta.qual |2013-10-14 13:40:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.hdr |2013-10-14 13:40:01| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.lib1.mappedmates |2013-10-14 13:40:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:40:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:41:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.unaligned.fasta.qual |2013-10-14 13:42:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.hdr |2013-10-14 13:42:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.lib1.mappedmates |2013-10-14 13:42:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:43:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:43:54| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.unaligned.fasta.qual |2013-10-14 13:45:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.hdr |2013-10-14 13:45:05| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.lib1.mappedmates |2013-10-14 13:45:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:45:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:46:27| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.unaligned.fasta.qual |2013-10-14 13:47:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.hdr |2013-10-14 13:47:35| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.lib1.mappedmates |2013-10-14 13:47:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:48:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:48:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.unaligned.fasta.qual |2013-10-14 13:50:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.hdr |2013-10-14 13:50:08| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.lib1.mappedmates |2013-10-14 13:50:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:50:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:51:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.unaligned.fasta.qual |2013-10-14 13:52:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.hdr |2013-10-14 13:52:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.lib1.mappedmates |2013-10-14 13:52:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:53:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:53:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.unaligned.fasta.qual |2013-10-14 13:55:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.hdr |2013-10-14 13:55:09| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.lib1.mappedmates |2013-10-14 13:55:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:55:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:56:28| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.unaligned.fasta.qual |2013-10-14 13:57:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.hdr |2013-10-14 13:57:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.lib1.mappedmates |2013-10-14 13:57:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 13:58:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 13:58:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.unaligned.fasta.qual |2013-10-14 14:00:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.hdr |2013-10-14 14:00:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.lib1.mappedmates |2013-10-14 14:00:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:00:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:01:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.unaligned.fasta.qual |2013-10-14 14:02:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.hdr |2013-10-14 14:02:42| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.lib1.mappedmates |2013-10-14 14:02:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:03:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:04:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.unaligned.fasta.qual |2013-10-14 14:05:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.hdr |2013-10-14 14:05:20| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.lib1.mappedmates |2013-10-14 14:05:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:06:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:06:39| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta.qual |2013-10-14 14:07:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr |2013-10-14 14:07:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates |2013-10-14 14:08:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:08:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:09:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.unaligned.fasta.qual |2013-10-14 14:10:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.hdr |2013-10-14 14:10:22| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.lib1.mappedmates |2013-10-14 14:10:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:11:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:11:37| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.unaligned.fasta.qual |2013-10-14 14:12:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.hdr |2013-10-14 14:12:57| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.lib1.mappedmates |2013-10-14 14:13:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:13:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:14:00| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.unaligned.fasta.qual |2013-10-14 14:15:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.hdr |2013-10-14 14:15:21| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.lib1.mappedmates |2013-10-14 14:15:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:16:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:16:26| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.unaligned.fasta.qual |2013-10-14 14:17:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.hdr |2013-10-14 14:17:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.lib1.mappedmates |2013-10-14 14:18:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:18:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:18:48| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.unaligned.fasta.qual |2013-10-14 14:20:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.hdr |2013-10-14 14:20:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.lib1.mappedmates |2013-10-14 14:20:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:21:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:21:17| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.unaligned.fasta.qual |2013-10-14 14:22:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.hdr |2013-10-14 14:22:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.lib1.mappedmates |2013-10-14 14:22:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:23:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:23:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.unaligned.fasta.qual |2013-10-14 14:25:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.hdr |2013-10-14 14:25:08| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.lib1.mappedmates |2013-10-14 14:25:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:25:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:26:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.unaligned.fasta.qual |2013-10-14 14:27:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.hdr |2013-10-14 14:27:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.lib1.mappedmates |2013-10-14 14:27:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:28:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:28:44| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.unaligned.fasta.qual |2013-10-14 14:30:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.hdr |2013-10-14 14:30:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.lib1.mappedmates |2013-10-14 14:30:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:30:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:31:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.unaligned.fasta.qual |2013-10-14 14:32:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.hdr |2013-10-14 14:32:33| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.lib1.mappedmates |2013-10-14 14:32:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:33:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:33:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.unaligned.fasta.qual |2013-10-14 14:34:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.hdr |2013-10-14 14:34:55| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.lib1.mappedmates |2013-10-14 14:35:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:35:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:36:22| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.unaligned.fasta.qual |2013-10-14 14:37:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.hdr |2013-10-14 14:37:23| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.lib1.mappedmates |2013-10-14 14:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:38:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:39:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.unaligned.fasta.qual |2013-10-14 14:40:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.hdr |2013-10-14 14:40:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.lib1.mappedmates |2013-10-14 14:42:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:44:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:45:03| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.unaligned.fasta.qual |2013-10-14 14:46:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.hdr |2013-10-14 14:46:35| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.lib1.mappedmates |2013-10-14 14:47:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:47:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:48:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.unaligned.fasta.qual |2013-10-14 14:49:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.hdr |2013-10-14 14:49:37| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.lib1.mappedmates |2013-10-14 14:49:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:50:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:50:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.unaligned.fasta.qual |2013-10-14 14:52:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.hdr |2013-10-14 14:52:17| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.lib1.mappedmates |2013-10-14 14:52:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:53:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:53:22| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.unaligned.fasta.qual |2013-10-14 14:54:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.hdr |2013-10-14 14:54:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.lib1.mappedmates |2013-10-14 14:55:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:55:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:56:06| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.unaligned.fasta.qual |2013-10-14 14:57:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.hdr |2013-10-14 14:57:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.lib1.mappedmates |2013-10-14 14:57:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 14:58:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 14:58:39| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.unaligned.fasta.qual |2013-10-14 15:00:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.hdr |2013-10-14 15:00:02| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.lib1.mappedmates |2013-10-14 15:00:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:00:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:01:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.unaligned.fasta.qual |2013-10-14 15:02:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.hdr |2013-10-14 15:02:31| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.lib1.mappedmates |2013-10-14 15:02:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:03:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:03:44| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.unaligned.fasta.qual |2013-10-14 15:05:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.hdr |2013-10-14 15:05:02| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.lib1.mappedmates |2013-10-14 15:05:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:05:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:06:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.unaligned.fasta.qual |2013-10-14 15:07:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.hdr |2013-10-14 15:07:30| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.lib1.mappedmates |2013-10-14 15:07:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:08:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:09:02| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.unaligned.fasta.qual |2013-10-14 15:10:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.hdr |2013-10-14 15:10:08| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.lib1.mappedmates |2013-10-14 15:10:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:10:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:11:45| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.unaligned.fasta.qual |2013-10-14 15:12:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.hdr |2013-10-14 15:12:48| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.lib1.mappedmates |2013-10-14 15:13:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:13:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:14:08| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.unaligned.fasta.qual |2013-10-14 15:15:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.hdr |2013-10-14 15:15:19| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.lib1.mappedmates |2013-10-14 15:15:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:16:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:16:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.unaligned.fasta.qual |2013-10-14 15:17:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.hdr |2013-10-14 15:17:55| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.lib1.mappedmates |2013-10-14 15:18:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:18:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:19:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.unaligned.fasta.qual |2013-10-14 15:20:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.hdr |2013-10-14 15:20:28| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.lib1.mappedmates |2013-10-14 15:20:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:21:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:21:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.unaligned.fasta.qual |2013-10-14 15:23:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.hdr |2013-10-14 15:23:00| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.lib1.mappedmates |2013-10-14 15:23:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:23:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:24:31| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.unaligned.fasta.qual |2013-10-14 15:25:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.hdr |2013-10-14 15:25:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.lib1.mappedmates |2013-10-14 15:25:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:26:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:27:01| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.unaligned.fasta.qual |2013-10-14 15:28:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.hdr |2013-10-14 15:28:03| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.lib1.mappedmates |2013-10-14 15:28:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:28:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:29:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.unaligned.fasta.qual |2013-10-14 15:30:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.hdr |2013-10-14 15:30:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.lib1.mappedmates |2013-10-14 15:30:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:31:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:32:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.unaligned.fasta.qual |2013-10-14 15:33:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.hdr |2013-10-14 15:33:06| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.lib1.mappedmates |2013-10-14 15:33:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:33:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:34:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.unaligned.fasta.qual |2013-10-14 15:35:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.hdr |2013-10-14 15:35:34| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.lib1.mappedmates |2013-10-14 15:35:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:38:34|# [MAPREADS] |2013-10-14 15:38:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:39:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:40:16| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.unaligned.fasta.qual |2013-10-14 15:41:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.hdr |2013-10-14 15:41:23| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.lib1.mappedmates |2013-10-14 15:41:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:42:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:42:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.unaligned.fasta.qual |2013-10-14 15:43:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.hdr |2013-10-14 15:43:37| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.lib1.mappedmates |2013-10-14 15:43:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:44:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:44:38| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.unaligned.fasta.qual |2013-10-14 15:45:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.hdr |2013-10-14 15:45:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.lib1.mappedmates |2013-10-14 15:46:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:46:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:46:54| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.unaligned.fasta.qual |2013-10-14 15:48:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.hdr |2013-10-14 15:48:14| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.lib1.mappedmates |2013-10-14 15:48:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:49:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:49:16| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.unaligned.fasta.qual |2013-10-14 15:50:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.hdr |2013-10-14 15:50:32| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.lib1.mappedmates |2013-10-14 15:50:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:51:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:51:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.unaligned.fasta.qual |2013-10-14 15:52:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.hdr |2013-10-14 15:52:49| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.lib1.mappedmates |2013-10-14 15:53:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:53:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:53:53| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.unaligned.fasta.qual |2013-10-14 15:55:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.hdr |2013-10-14 15:55:17| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.lib1.mappedmates |2013-10-14 15:55:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:56:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 15:56:49| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.unaligned.fasta.qual |2013-10-14 15:57:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.hdr |2013-10-14 15:57:50| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.lib1.mappedmates |2013-10-14 15:57:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 15:58:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:00:47| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.unaligned.fasta.qual |2013-10-14 16:00:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.hdr |2013-10-14 16:00:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.lib1.mappedmates |2013-10-14 16:01:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:01:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:01:51| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.unaligned.fasta.qual |2013-10-14 16:03:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.hdr |2013-10-14 16:03:15| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.lib1.mappedmates |2013-10-14 16:03:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:04:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:04:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.unaligned.fasta.qual |2013-10-14 16:05:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.hdr |2013-10-14 16:05:45| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.lib1.mappedmates |2013-10-14 16:06:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:06:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:06:52| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.unaligned.fasta.qual |2013-10-14 16:08:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.hdr |2013-10-14 16:08:15| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.lib1.mappedmates |2013-10-14 16:08:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:09:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:09:20| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.unaligned.fasta.qual |2013-10-14 16:10:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.hdr |2013-10-14 16:10:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.lib1.mappedmates |2013-10-14 16:11:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:11:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:11:49| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.unaligned.fasta.qual |2013-10-14 16:13:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.hdr |2013-10-14 16:13:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.lib1.mappedmates |2013-10-14 16:13:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:14:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:14:17| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.unaligned.fasta.qual |2013-10-14 16:15:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.hdr |2013-10-14 16:15:40| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.lib1.mappedmates |2013-10-14 16:15:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:16:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:16:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.unaligned.fasta.qual |2013-10-14 16:18:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.hdr |2013-10-14 16:18:07| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.lib1.mappedmates |2013-10-14 16:18:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:18:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:19:12| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.unaligned.fasta.qual |2013-10-14 16:20:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.hdr |2013-10-14 16:20:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.lib1.mappedmates |2013-10-14 16:20:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:21:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:21:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.unaligned.fasta.qual |2013-10-14 16:23:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.hdr |2013-10-14 16:23:03| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.lib1.mappedmates |2013-10-14 16:23:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:23:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:24:08| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.unaligned.fasta.qual |2013-10-14 16:25:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.hdr |2013-10-14 16:25:30| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.lib1.mappedmates |2013-10-14 16:25:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:26:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:26:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.unaligned.fasta.qual |2013-10-14 16:28:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.hdr |2013-10-14 16:28:03| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.lib1.mappedmates |2013-10-14 16:28:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:28:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:29:22| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.unaligned.fasta.qual |2013-10-14 16:30:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.hdr |2013-10-14 16:30:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.lib1.mappedmates |2013-10-14 16:30:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:31:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:32:11| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.unaligned.fasta.qual |2013-10-14 16:33:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.hdr |2013-10-14 16:33:19| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.lib1.mappedmates |2013-10-14 16:33:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:34:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:34:43| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.unaligned.fasta.qual |2013-10-14 16:35:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.hdr |2013-10-14 16:35:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.lib1.mappedmates |2013-10-14 16:36:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:36:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:37:21| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.unaligned.fasta.qual |2013-10-14 16:38:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.hdr |2013-10-14 16:38:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.lib1.mappedmates |2013-10-14 16:38:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:39:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:39:55| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.unaligned.fasta.qual |2013-10-14 16:41:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.hdr |2013-10-14 16:41:14| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.lib1.mappedmates |2013-10-14 16:41:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:42:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:42:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.unaligned.fasta.qual |2013-10-14 16:43:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.hdr |2013-10-14 16:43:55| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.lib1.mappedmates |2013-10-14 16:44:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:44:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:45:07| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.unaligned.fasta.qual |2013-10-14 16:46:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.hdr |2013-10-14 16:46:23| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.lib1.mappedmates |2013-10-14 16:46:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:47:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:47:36| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.unaligned.fasta.qual |2013-10-14 16:48:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.hdr |2013-10-14 16:48:52| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.lib1.mappedmates |2013-10-14 16:49:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:49:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:50:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.unaligned.fasta.qual |2013-10-14 16:51:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.hdr |2013-10-14 16:51:21| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.lib1.mappedmates |2013-10-14 16:51:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:52:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:52:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.unaligned.fasta.qual |2013-10-14 16:53:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.hdr |2013-10-14 16:53:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.lib1.mappedmates |2013-10-14 16:54:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:54:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:55:10| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.unaligned.fasta.qual |2013-10-14 16:56:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.hdr |2013-10-14 16:56:31| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.lib1.mappedmates |2013-10-14 16:56:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 16:57:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 16:58:26| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.unaligned.fasta.qual |2013-10-14 16:59:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.hdr |2013-10-14 16:59:20| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.lib1.mappedmates |2013-10-14 16:59:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:00:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:01:35| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.unaligned.fasta.qual |2013-10-14 17:02:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.hdr |2013-10-14 17:02:21| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.lib1.mappedmates |2013-10-14 17:02:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:03:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:03:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.unaligned.fasta.qual |2013-10-14 17:04:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.hdr |2013-10-14 17:04:54| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.lib1.mappedmates |2013-10-14 17:05:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:05:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:06:03| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.unaligned.fasta.qual |2013-10-14 17:07:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.hdr |2013-10-14 17:07:33| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.lib1.mappedmates |2013-10-14 17:07:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:08:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:08:42| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.unaligned.fasta.qual |2013-10-14 17:10:11| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.hdr |2013-10-14 17:10:11| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.lib1.mappedmates |2013-10-14 17:10:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:11:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:11:15| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.unaligned.fasta.qual |2013-10-14 17:12:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.hdr |2013-10-14 17:12:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.lib1.mappedmates |2013-10-14 17:13:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:13:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:13:50| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.unaligned.fasta.qual |2013-10-14 17:15:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.hdr |2013-10-14 17:15:20| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.lib1.mappedmates |2013-10-14 17:55:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 17:56:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 17:58:52| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.unaligned.fasta.qual |2013-10-14 17:59:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.hdr |2013-10-14 17:59:37| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.lib1.mappedmates |2013-10-14 17:59:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:00:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:03:03| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.unaligned.fasta.qual |2013-10-14 18:04:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.hdr |2013-10-14 18:04:29| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.lib1.mappedmates |2013-10-14 18:04:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:05:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:06:59| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.unaligned.fasta.qual |2013-10-14 18:07:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.hdr |2013-10-14 18:07:53| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.lib1.mappedmates |2013-10-14 18:08:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:08:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:10:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.unaligned.fasta.qual |2013-10-14 18:11:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.hdr |2013-10-14 18:11:19| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.lib1.mappedmates |2013-10-14 18:11:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:12:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:12:47| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.unaligned.fasta.qual |2013-10-14 18:14:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.hdr |2013-10-14 18:14:13| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.lib1.mappedmates |2013-10-14 18:14:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:15:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:15:57| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.unaligned.fasta.qual |2013-10-14 18:17:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.hdr |2013-10-14 18:17:22| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.lib1.mappedmates |2013-10-14 18:18:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:25:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:28:29| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.unaligned.fasta.qual |2013-10-14 18:28:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.hdr |2013-10-14 18:28:35| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.lib1.mappedmates |2013-10-14 18:28:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:29:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:30:05| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.unaligned.fasta.qual |2013-10-14 18:31:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.hdr |2013-10-14 18:31:36| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.lib1.mappedmates |2013-10-14 18:31:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:32:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:32:58| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.unaligned.fasta.qual |2013-10-14 18:34:26| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.hdr |2013-10-14 18:34:27| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.lib1.mappedmates |2013-10-14 18:34:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:35:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:35:46| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.unaligned.fasta.qual |2013-10-14 18:37:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.hdr |2013-10-14 18:37:14| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.lib1.mappedmates |2013-10-14 18:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:38:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:38:32| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.unaligned.fasta.qual |2013-10-14 18:39:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.hdr |2013-10-14 18:39:57| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.lib1.mappedmates |2013-10-14 18:40:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:41:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:41:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.unaligned.fasta.qual |2013-10-14 18:42:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.hdr |2013-10-14 18:42:44| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.lib1.mappedmates |2013-10-14 18:43:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:43:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:43:59| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.unaligned.fasta.qual |2013-10-14 18:45:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.hdr |2013-10-14 18:45:24| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.lib1.mappedmates |2013-10-14 18:45:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:46:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:46:42| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.unaligned.fasta.qual |2013-10-14 18:48:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.hdr |2013-10-14 18:48:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.lib1.mappedmates |2013-10-14 18:48:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX |2013-10-14 18:49:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/bowtie -p 16 -l 25 -e 140 --best --strata -m 10 -k 1 --un /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/IDX /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.bout |2013-10-14 18:49:24| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. convertFastqToFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.unaligned.seq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.unaligned.fasta.qual |2013-10-14 18:50:48| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.mappedmates >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.hdr |2013-10-14 18:50:49| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.lib1.mappedmates |2013-10-14 18:50:57|# [FINDORFS] |2013-10-14 18:50:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.25.asm.contig |2013-10-14 18:50:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-14 19:46:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka --prefix abyss.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.25.asm.contig |2013-10-14 19:46:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka/abyss.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.fna |2013-10-14 19:46:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka/abyss.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.faa |2013-10-14 19:46:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.gene.cvg |2013-10-14 19:46:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.gene.map |2013-10-14 19:46:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna |2013-10-14 19:46:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna |2013-10-14 19:46:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna.bnk |2013-10-14 19:46:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna.bnk |2013-10-14 19:46:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa |2013-10-14 19:46:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa |2013-10-14 19:46:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa.bnk |2013-10-14 19:46:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa.bnk |2013-10-14 19:46:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg |2013-10-14 19:46:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg |2013-10-14 19:46:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map |2013-10-14 19:46:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map |2013-10-14 19:46:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.faa |2013-10-14 19:46:41| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.35.asm.contig |2013-10-14 19:46:41| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-14 20:43:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka --prefix abyss.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.35.asm.contig |2013-10-14 20:43:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka/abyss.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.fna |2013-10-14 20:43:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka/abyss.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.faa |2013-10-14 20:43:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.gene.cvg |2013-10-14 20:43:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.gene.map |2013-10-14 20:43:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna |2013-10-14 20:43:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna |2013-10-14 20:43:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna.bnk |2013-10-14 20:43:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna.bnk |2013-10-14 20:43:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa |2013-10-14 20:43:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa |2013-10-14 20:43:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa.bnk |2013-10-14 20:43:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa.bnk |2013-10-14 20:43:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg |2013-10-14 20:43:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg |2013-10-14 20:43:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map |2013-10-14 20:43:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map |2013-10-14 20:43:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.faa |2013-10-14 20:43:23| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.41.asm.contig |2013-10-14 20:43:23| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-14 21:40:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka --prefix abyss.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.41.asm.contig |2013-10-14 21:40:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka/abyss.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.fna |2013-10-14 21:40:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka/abyss.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.faa |2013-10-14 21:40:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.gene.cvg |2013-10-14 21:40:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.gene.map |2013-10-14 21:40:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna |2013-10-14 21:40:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna |2013-10-14 21:40:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna.bnk |2013-10-14 21:40:26| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna.bnk |2013-10-14 21:40:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa |2013-10-14 21:40:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa |2013-10-14 21:40:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa.bnk |2013-10-14 21:40:28| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa.bnk |2013-10-14 21:40:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg |2013-10-14 21:40:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg |2013-10-14 21:40:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map |2013-10-14 21:40:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map |2013-10-14 21:40:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.faa |2013-10-14 21:40:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.45.asm.contig |2013-10-14 21:40:29| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-14 22:37:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka --prefix abyss.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.45.asm.contig |2013-10-14 22:37:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka/abyss.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.fna |2013-10-14 22:37:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka/abyss.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.faa |2013-10-14 22:37:47| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.gene.cvg |2013-10-14 22:37:47| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.gene.map |2013-10-14 22:37:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna |2013-10-14 22:37:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna |2013-10-14 22:37:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna.bnk |2013-10-14 22:37:49| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna.bnk |2013-10-14 22:37:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa |2013-10-14 22:37:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa |2013-10-14 22:37:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa.bnk |2013-10-14 22:37:51| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa.bnk |2013-10-14 22:37:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg |2013-10-14 22:37:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg |2013-10-14 22:37:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map |2013-10-14 22:37:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map |2013-10-14 22:37:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.faa |2013-10-14 22:37:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.55.asm.contig |2013-10-14 22:37:52| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-14 23:34:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka --prefix abyss.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.55.asm.contig |2013-10-14 23:34:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka/abyss.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.fna |2013-10-14 23:34:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka/abyss.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.faa |2013-10-14 23:34:29| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.gene.cvg |2013-10-14 23:34:29| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.gene.map |2013-10-14 23:34:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna |2013-10-14 23:34:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna |2013-10-14 23:34:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna.bnk |2013-10-14 23:34:31| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna.bnk |2013-10-14 23:34:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa |2013-10-14 23:34:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa |2013-10-14 23:34:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa.bnk |2013-10-14 23:34:32| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa.bnk |2013-10-14 23:34:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg |2013-10-14 23:34:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg |2013-10-14 23:34:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map |2013-10-14 23:34:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map |2013-10-14 23:34:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.faa |2013-10-14 23:34:33| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.65.asm.contig |2013-10-14 23:34:33| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 00:31:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka --prefix abyss.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.65.asm.contig |2013-10-15 00:31:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka/abyss.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.fna |2013-10-15 00:31:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka/abyss.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.faa |2013-10-15 00:31:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.gene.cvg |2013-10-15 00:31:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.gene.map |2013-10-15 00:31:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna |2013-10-15 00:31:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna |2013-10-15 00:31:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna.bnk |2013-10-15 00:31:40| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna.bnk |2013-10-15 00:31:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa |2013-10-15 00:31:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa |2013-10-15 00:31:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa.bnk |2013-10-15 00:31:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa.bnk |2013-10-15 00:31:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg |2013-10-15 00:31:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg |2013-10-15 00:31:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map |2013-10-15 00:31:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map |2013-10-15 00:31:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.faa |2013-10-15 00:31:45| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.75.asm.contig |2013-10-15 00:31:45| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 01:29:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka --prefix abyss.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.75.asm.contig |2013-10-15 01:29:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka/abyss.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.fna |2013-10-15 01:29:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka/abyss.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.faa |2013-10-15 01:29:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.gene.cvg |2013-10-15 01:29:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.gene.map |2013-10-15 01:29:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna |2013-10-15 01:29:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna |2013-10-15 01:29:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna.bnk |2013-10-15 01:29:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna.bnk |2013-10-15 01:29:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa |2013-10-15 01:29:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa |2013-10-15 01:29:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa.bnk |2013-10-15 01:29:59| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa.bnk |2013-10-15 01:29:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg |2013-10-15 01:29:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg |2013-10-15 01:29:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map |2013-10-15 01:30:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map |2013-10-15 01:30:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.faa |2013-10-15 01:30:00| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.85.asm.contig |2013-10-15 01:30:00| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 02:28:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka --prefix abyss.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.85.asm.contig |2013-10-15 02:28:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka/abyss.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.fna |2013-10-15 02:28:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka/abyss.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.faa |2013-10-15 02:28:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.gene.cvg |2013-10-15 02:28:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.gene.map |2013-10-15 02:28:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna |2013-10-15 02:28:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna |2013-10-15 02:28:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna.bnk |2013-10-15 02:28:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna.bnk |2013-10-15 02:28:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa |2013-10-15 02:28:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa |2013-10-15 02:28:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa.bnk |2013-10-15 02:28:47| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa.bnk |2013-10-15 02:28:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg |2013-10-15 02:28:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg |2013-10-15 02:28:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map |2013-10-15 02:28:48| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map |2013-10-15 02:28:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.faa |2013-10-15 02:28:48| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.95.asm.contig |2013-10-15 02:28:48| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 03:30:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka --prefix abyss.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.95.asm.contig |2013-10-15 03:30:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka/abyss.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.fna |2013-10-15 03:30:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka/abyss.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.faa |2013-10-15 03:30:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.gene.cvg |2013-10-15 03:30:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.gene.map |2013-10-15 03:30:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna |2013-10-15 03:30:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna |2013-10-15 03:30:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna.bnk |2013-10-15 03:30:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna.bnk |2013-10-15 03:30:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa |2013-10-15 03:30:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa |2013-10-15 03:30:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa.bnk |2013-10-15 03:30:59| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa.bnk |2013-10-15 03:30:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg |2013-10-15 03:30:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg |2013-10-15 03:30:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map |2013-10-15 03:30:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map |2013-10-15 03:31:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.faa |2013-10-15 03:31:00| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.105.asm.contig |2013-10-15 03:31:00| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 04:38:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka --prefix idba-ud.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.105.asm.contig |2013-10-15 04:38:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka/idba-ud.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.fna |2013-10-15 04:38:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka/idba-ud.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.faa |2013-10-15 04:38:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.gene.cvg |2013-10-15 04:38:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.gene.map |2013-10-15 04:38:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna |2013-10-15 04:38:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna |2013-10-15 04:38:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna.bnk |2013-10-15 04:38:44| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna.bnk |2013-10-15 04:38:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa |2013-10-15 04:38:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa |2013-10-15 04:38:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa.bnk |2013-10-15 04:38:45| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa.bnk |2013-10-15 04:38:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg |2013-10-15 04:38:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg |2013-10-15 04:38:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map |2013-10-15 04:38:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map |2013-10-15 04:38:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.faa |2013-10-15 04:38:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.25.asm.contig |2013-10-15 04:38:46| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 06:06:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka --prefix idba-ud.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.25.asm.contig |2013-10-15 06:06:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka/idba-ud.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.fna |2013-10-15 06:06:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka/idba-ud.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.faa |2013-10-15 06:06:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.gene.cvg |2013-10-15 06:06:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.gene.map |2013-10-15 06:06:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna |2013-10-15 06:06:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna |2013-10-15 06:06:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna.bnk |2013-10-15 06:06:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna.bnk |2013-10-15 06:06:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa |2013-10-15 06:06:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa |2013-10-15 06:06:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa.bnk |2013-10-15 06:06:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa.bnk |2013-10-15 06:06:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg |2013-10-15 06:06:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg |2013-10-15 06:06:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map |2013-10-15 06:06:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map |2013-10-15 06:06:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.faa |2013-10-15 06:06:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.35.asm.contig |2013-10-15 06:06:35| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 07:32:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka --prefix idba-ud.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.35.asm.contig |2013-10-15 07:32:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka/idba-ud.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.fna |2013-10-15 07:32:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka/idba-ud.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.faa |2013-10-15 07:32:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.gene.cvg |2013-10-15 07:32:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.gene.map |2013-10-15 07:32:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna |2013-10-15 07:32:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna |2013-10-15 07:32:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna.bnk |2013-10-15 07:33:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna.bnk |2013-10-15 07:33:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa |2013-10-15 07:33:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa |2013-10-15 07:33:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa.bnk |2013-10-15 07:33:03| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa.bnk |2013-10-15 07:33:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg |2013-10-15 07:33:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg |2013-10-15 07:33:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map |2013-10-15 07:33:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map |2013-10-15 07:33:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.faa |2013-10-15 07:33:04| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.41.asm.contig |2013-10-15 07:33:04| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 08:56:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka --prefix idba-ud.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.41.asm.contig |2013-10-15 08:56:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka/idba-ud.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.fna |2013-10-15 08:56:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka/idba-ud.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.faa |2013-10-15 08:56:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.gene.cvg |2013-10-15 08:56:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.gene.map |2013-10-15 08:56:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna |2013-10-15 08:56:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna |2013-10-15 08:56:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna.bnk |2013-10-15 08:56:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna.bnk |2013-10-15 08:56:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa |2013-10-15 08:56:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa |2013-10-15 08:56:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa.bnk |2013-10-15 08:56:53| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa.bnk |2013-10-15 08:56:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg |2013-10-15 08:56:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg |2013-10-15 08:56:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map |2013-10-15 08:56:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map |2013-10-15 08:56:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.faa |2013-10-15 08:56:54| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.45.asm.contig |2013-10-15 08:56:54| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 09:31:38|# [FINDORFS] |2013-10-15 09:31:38| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.45.asm.contig |2013-10-15 09:31:38| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 11:05:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka --prefix idba-ud.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.45.asm.contig |2013-10-15 11:05:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka/idba-ud.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.fna |2013-10-15 11:05:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka/idba-ud.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.faa |2013-10-15 11:05:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.gene.cvg |2013-10-15 11:05:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.gene.map |2013-10-15 11:05:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna |2013-10-15 11:05:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna |2013-10-15 11:05:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna.bnk |2013-10-15 11:05:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna.bnk |2013-10-15 11:05:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa |2013-10-15 11:05:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa |2013-10-15 11:05:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa.bnk |2013-10-15 11:05:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa.bnk |2013-10-15 11:05:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg |2013-10-15 11:05:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg |2013-10-15 11:05:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map |2013-10-15 11:05:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map |2013-10-15 11:05:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.faa |2013-10-15 11:05:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.55.asm.contig |2013-10-15 11:05:35| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:09:14|# [FINDORFS] |2013-10-15 12:09:14| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.55.asm.contig |2013-10-15 12:09:14| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:10:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka --prefix idba-ud.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.55.asm.contig |2013-10-15 12:10:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka/idba-ud.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.fna |2013-10-15 12:10:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka/idba-ud.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.faa |2013-10-15 12:10:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.gene.cvg |2013-10-15 12:10:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.gene.map |2013-10-15 12:10:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna |2013-10-15 12:10:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna |2013-10-15 12:10:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna.bnk |2013-10-15 12:10:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna.bnk |2013-10-15 12:10:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa |2013-10-15 12:10:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa |2013-10-15 12:10:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa.bnk |2013-10-15 12:10:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa.bnk |2013-10-15 12:10:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg |2013-10-15 12:10:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg |2013-10-15 12:10:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map |2013-10-15 12:10:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map |2013-10-15 12:10:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.faa |2013-10-15 12:10:17| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.65.asm.contig |2013-10-15 12:10:17| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:11:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka --prefix idba-ud.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.65.asm.contig |2013-10-15 12:11:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka/idba-ud.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.fna |2013-10-15 12:11:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka/idba-ud.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.faa |2013-10-15 12:11:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.gene.cvg |2013-10-15 12:11:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.gene.map |2013-10-15 12:11:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna |2013-10-15 12:11:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna |2013-10-15 12:11:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna.bnk |2013-10-15 12:11:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna.bnk |2013-10-15 12:11:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa |2013-10-15 12:11:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa |2013-10-15 12:11:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa.bnk |2013-10-15 12:11:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa.bnk |2013-10-15 12:11:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg |2013-10-15 12:11:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg |2013-10-15 12:11:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map |2013-10-15 12:11:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map |2013-10-15 12:11:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.faa |2013-10-15 12:11:18| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.75.asm.contig |2013-10-15 12:11:18| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:12:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka --prefix idba-ud.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.75.asm.contig |2013-10-15 12:12:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka/idba-ud.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.fna |2013-10-15 12:12:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka/idba-ud.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.faa |2013-10-15 12:12:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.gene.cvg |2013-10-15 12:12:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.gene.map |2013-10-15 12:12:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna |2013-10-15 12:12:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna |2013-10-15 12:12:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna.bnk |2013-10-15 12:12:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna.bnk |2013-10-15 12:12:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa |2013-10-15 12:12:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa |2013-10-15 12:12:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa.bnk |2013-10-15 12:12:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa.bnk |2013-10-15 12:12:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg |2013-10-15 12:12:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg |2013-10-15 12:12:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map |2013-10-15 12:12:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map |2013-10-15 12:12:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.faa |2013-10-15 12:12:18| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.85.asm.contig |2013-10-15 12:12:18| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:13:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka --prefix idba-ud.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.85.asm.contig |2013-10-15 12:13:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka/idba-ud.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.fna |2013-10-15 12:13:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka/idba-ud.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.faa |2013-10-15 12:13:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.gene.cvg |2013-10-15 12:13:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.gene.map |2013-10-15 12:13:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna |2013-10-15 12:13:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna |2013-10-15 12:13:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna.bnk |2013-10-15 12:13:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna.bnk |2013-10-15 12:13:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa |2013-10-15 12:13:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa |2013-10-15 12:13:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa.bnk |2013-10-15 12:13:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa.bnk |2013-10-15 12:13:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg |2013-10-15 12:13:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg |2013-10-15 12:13:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map |2013-10-15 12:13:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map |2013-10-15 12:13:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.faa |2013-10-15 12:13:17| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.95.asm.contig |2013-10-15 12:13:17| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:14:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka --prefix idba-ud.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.95.asm.contig |2013-10-15 12:14:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka/idba-ud.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.fna |2013-10-15 12:14:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka/idba-ud.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.faa |2013-10-15 12:14:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.gene.cvg |2013-10-15 12:14:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.gene.map |2013-10-15 12:14:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna |2013-10-15 12:14:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna |2013-10-15 12:14:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna.bnk |2013-10-15 12:14:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna.bnk |2013-10-15 12:14:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa |2013-10-15 12:14:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa |2013-10-15 12:14:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa.bnk |2013-10-15 12:14:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa.bnk |2013-10-15 12:14:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg |2013-10-15 12:14:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg |2013-10-15 12:14:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map |2013-10-15 12:14:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map |2013-10-15 12:14:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.faa |2013-10-15 12:14:17| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-10-15 12:14:17| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:14:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka --prefix masurca.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-10-15 12:14:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka/masurca.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.fna |2013-10-15 12:14:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka/masurca.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.faa |2013-10-15 12:14:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.gene.cvg |2013-10-15 12:14:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.gene.map |2013-10-15 12:14:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna |2013-10-15 12:14:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna |2013-10-15 12:14:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna.bnk |2013-10-15 12:14:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna.bnk |2013-10-15 12:14:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa |2013-10-15 12:14:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa |2013-10-15 12:14:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa.bnk |2013-10-15 12:14:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa.bnk |2013-10-15 12:14:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg |2013-10-15 12:14:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg |2013-10-15 12:14:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map |2013-10-15 12:14:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map |2013-10-15 12:14:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.faa |2013-10-15 12:14:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.125.asm.contig |2013-10-15 12:14:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:15:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka --prefix masurca.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.125.asm.contig |2013-10-15 12:15:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka/masurca.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.fna |2013-10-15 12:15:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka/masurca.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.faa |2013-10-15 12:15:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.gene.cvg |2013-10-15 12:15:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.gene.map |2013-10-15 12:15:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna |2013-10-15 12:15:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna |2013-10-15 12:15:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna.bnk |2013-10-15 12:15:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna.bnk |2013-10-15 12:15:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa |2013-10-15 12:15:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa |2013-10-15 12:15:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa.bnk |2013-10-15 12:15:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa.bnk |2013-10-15 12:15:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg |2013-10-15 12:15:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg |2013-10-15 12:15:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map |2013-10-15 12:15:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map |2013-10-15 12:15:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.faa |2013-10-15 12:15:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.25.asm.contig |2013-10-15 12:15:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:16:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka --prefix masurca.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.25.asm.contig |2013-10-15 12:16:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka/masurca.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.fna |2013-10-15 12:16:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka/masurca.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.faa |2013-10-15 12:16:18| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.gene.cvg |2013-10-15 12:16:18| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.gene.map |2013-10-15 12:16:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna |2013-10-15 12:16:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna |2013-10-15 12:16:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna.bnk |2013-10-15 12:16:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna.bnk |2013-10-15 12:16:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa |2013-10-15 12:16:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa |2013-10-15 12:16:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa.bnk |2013-10-15 12:16:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa.bnk |2013-10-15 12:16:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg |2013-10-15 12:16:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg |2013-10-15 12:16:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map |2013-10-15 12:16:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map |2013-10-15 12:16:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.faa |2013-10-15 12:16:20| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.35.asm.contig |2013-10-15 12:16:20| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:17:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka --prefix masurca.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.35.asm.contig |2013-10-15 12:17:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka/masurca.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.fna |2013-10-15 12:17:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka/masurca.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.faa |2013-10-15 12:17:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.gene.cvg |2013-10-15 12:17:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.gene.map |2013-10-15 12:17:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna |2013-10-15 12:17:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna |2013-10-15 12:17:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna.bnk |2013-10-15 12:17:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna.bnk |2013-10-15 12:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa |2013-10-15 12:17:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa |2013-10-15 12:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa.bnk |2013-10-15 12:17:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa.bnk |2013-10-15 12:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg |2013-10-15 12:17:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg |2013-10-15 12:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map |2013-10-15 12:17:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map |2013-10-15 12:17:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.faa |2013-10-15 12:17:02| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.41.asm.contig |2013-10-15 12:17:02| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:17:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka --prefix masurca.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.41.asm.contig |2013-10-15 12:17:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka/masurca.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.fna |2013-10-15 12:17:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka/masurca.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.faa |2013-10-15 12:17:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.gene.cvg |2013-10-15 12:17:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.gene.map |2013-10-15 12:17:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna |2013-10-15 12:17:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna |2013-10-15 12:17:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna.bnk |2013-10-15 12:18:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna.bnk |2013-10-15 12:18:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa |2013-10-15 12:18:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa |2013-10-15 12:18:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa.bnk |2013-10-15 12:18:08| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa.bnk |2013-10-15 12:18:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg |2013-10-15 12:18:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg |2013-10-15 12:18:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map |2013-10-15 12:18:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map |2013-10-15 12:18:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.faa |2013-10-15 12:18:08| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.45.asm.contig |2013-10-15 12:18:08| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 12:19:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka --prefix masurca.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.45.asm.contig |2013-10-15 12:19:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka/masurca.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.fna |2013-10-15 12:19:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka/masurca.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.faa |2013-10-15 12:19:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.gene.cvg |2013-10-15 12:19:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.gene.map |2013-10-15 12:19:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna |2013-10-15 12:19:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna |2013-10-15 12:19:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna.bnk |2013-10-15 12:38:30| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna.bnk |2013-10-15 12:38:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa |2013-10-15 12:38:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa |2013-10-15 12:38:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa.bnk |2013-10-15 12:38:31| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa.bnk |2013-10-15 12:38:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg |2013-10-15 12:38:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg |2013-10-15 12:38:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map |2013-10-15 12:38:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map |2013-10-15 12:38:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.faa |2013-10-15 12:38:31| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.55.asm.contig |2013-10-15 12:38:31| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:17:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka --prefix masurca.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.55.asm.contig |2013-10-15 13:17:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka/masurca.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.fna |2013-10-15 13:17:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka/masurca.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.faa |2013-10-15 13:17:02| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.gene.cvg |2013-10-15 13:17:02| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.gene.map |2013-10-15 13:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna |2013-10-15 13:17:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna |2013-10-15 13:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna.bnk |2013-10-15 13:17:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna.bnk |2013-10-15 13:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa |2013-10-15 13:17:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa |2013-10-15 13:17:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa.bnk |2013-10-15 13:17:03| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa.bnk |2013-10-15 13:17:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg |2013-10-15 13:17:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg |2013-10-15 13:17:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map |2013-10-15 13:17:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map |2013-10-15 13:17:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.faa |2013-10-15 13:17:03| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.65.asm.contig |2013-10-15 13:17:03| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:17:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka --prefix masurca.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.65.asm.contig |2013-10-15 13:17:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka/masurca.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.fna |2013-10-15 13:17:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka/masurca.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.faa |2013-10-15 13:17:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.gene.cvg |2013-10-15 13:17:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.gene.map |2013-10-15 13:17:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna |2013-10-15 13:17:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna |2013-10-15 13:17:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna.bnk |2013-10-15 13:17:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna.bnk |2013-10-15 13:17:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa |2013-10-15 13:17:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa |2013-10-15 13:17:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa.bnk |2013-10-15 13:17:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa.bnk |2013-10-15 13:17:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg |2013-10-15 13:17:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg |2013-10-15 13:17:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map |2013-10-15 13:17:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map |2013-10-15 13:17:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.faa |2013-10-15 13:17:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.75.asm.contig |2013-10-15 13:17:47| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:18:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka --prefix masurca.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.75.asm.contig |2013-10-15 13:18:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka/masurca.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.fna |2013-10-15 13:18:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka/masurca.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.faa |2013-10-15 13:18:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.gene.cvg |2013-10-15 13:18:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.gene.map |2013-10-15 13:18:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna |2013-10-15 13:18:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna |2013-10-15 13:18:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna.bnk |2013-10-15 13:18:27| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna.bnk |2013-10-15 13:18:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa |2013-10-15 13:18:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa |2013-10-15 13:18:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa.bnk |2013-10-15 13:18:28| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa.bnk |2013-10-15 13:18:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg |2013-10-15 13:18:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg |2013-10-15 13:18:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map |2013-10-15 13:18:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map |2013-10-15 13:18:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.faa |2013-10-15 13:18:28| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.85.asm.contig |2013-10-15 13:18:28| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:19:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka --prefix masurca.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.85.asm.contig |2013-10-15 13:19:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka/masurca.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.fna |2013-10-15 13:19:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka/masurca.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.faa |2013-10-15 13:19:09| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.gene.cvg |2013-10-15 13:19:09| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.gene.map |2013-10-15 13:19:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna |2013-10-15 13:19:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna |2013-10-15 13:19:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna.bnk |2013-10-15 13:19:11| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna.bnk |2013-10-15 13:19:11| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa |2013-10-15 13:19:11| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa |2013-10-15 13:19:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa.bnk |2013-10-15 13:19:13| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa.bnk |2013-10-15 13:19:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg |2013-10-15 13:19:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg |2013-10-15 13:19:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map |2013-10-15 13:19:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map |2013-10-15 13:19:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.faa |2013-10-15 13:19:14| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.95.asm.contig |2013-10-15 13:19:14| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:19:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka --prefix masurca.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.95.asm.contig |2013-10-15 13:19:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka/masurca.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.fna |2013-10-15 13:19:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka/masurca.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.faa |2013-10-15 13:19:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.gene.cvg |2013-10-15 13:19:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.gene.map |2013-10-15 13:19:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna |2013-10-15 13:19:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna |2013-10-15 13:19:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna.bnk |2013-10-15 13:19:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna.bnk |2013-10-15 13:19:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa |2013-10-15 13:19:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa |2013-10-15 13:19:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa.bnk |2013-10-15 13:20:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa.bnk |2013-10-15 13:20:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg |2013-10-15 13:20:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg |2013-10-15 13:20:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map |2013-10-15 13:20:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map |2013-10-15 13:20:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.faa |2013-10-15 13:20:00| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.105.asm.contig |2013-10-15 13:20:00| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:20:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka --prefix mira.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.105.asm.contig |2013-10-15 13:20:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka/mira.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.fna |2013-10-15 13:20:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka/mira.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.faa |2013-10-15 13:20:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.gene.cvg |2013-10-15 13:20:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.gene.map |2013-10-15 13:20:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna |2013-10-15 13:20:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna |2013-10-15 13:20:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna.bnk |2013-10-15 13:20:45| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna.bnk |2013-10-15 13:20:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa |2013-10-15 13:20:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa |2013-10-15 13:20:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa.bnk |2013-10-15 13:20:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa.bnk |2013-10-15 13:20:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg |2013-10-15 13:20:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg |2013-10-15 13:20:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map |2013-10-15 13:20:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map |2013-10-15 13:20:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.faa |2013-10-15 13:20:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.125.asm.contig |2013-10-15 13:20:46| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:21:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka --prefix mira.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.125.asm.contig |2013-10-15 13:21:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka/mira.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.fna |2013-10-15 13:21:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka/mira.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.faa |2013-10-15 13:21:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.gene.cvg |2013-10-15 13:21:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.gene.map |2013-10-15 13:21:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna |2013-10-15 13:21:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna |2013-10-15 13:21:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna.bnk |2013-10-15 13:21:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna.bnk |2013-10-15 13:21:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa |2013-10-15 13:21:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa |2013-10-15 13:21:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa.bnk |2013-10-15 13:21:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa.bnk |2013-10-15 13:21:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg |2013-10-15 13:21:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg |2013-10-15 13:21:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map |2013-10-15 13:21:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map |2013-10-15 13:21:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.faa |2013-10-15 13:21:38| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.25.asm.contig |2013-10-15 13:21:38| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:22:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka --prefix mira.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.25.asm.contig |2013-10-15 13:22:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka/mira.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.fna |2013-10-15 13:22:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka/mira.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.faa |2013-10-15 13:22:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.gene.cvg |2013-10-15 13:22:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.gene.map |2013-10-15 13:22:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna |2013-10-15 13:22:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna |2013-10-15 13:22:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna.bnk |2013-10-15 13:22:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna.bnk |2013-10-15 13:22:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa |2013-10-15 13:22:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa |2013-10-15 13:22:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa.bnk |2013-10-15 13:22:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa.bnk |2013-10-15 13:22:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg |2013-10-15 13:22:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg |2013-10-15 13:22:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map |2013-10-15 13:22:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map |2013-10-15 13:22:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.faa |2013-10-15 13:22:24| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.35.asm.contig |2013-10-15 13:22:24| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:23:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka --prefix mira.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.35.asm.contig |2013-10-15 13:23:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka/mira.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.fna |2013-10-15 13:23:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka/mira.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.faa |2013-10-15 13:23:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.gene.cvg |2013-10-15 13:23:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.gene.map |2013-10-15 13:23:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna |2013-10-15 13:23:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna |2013-10-15 13:23:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna.bnk |2013-10-15 13:23:09| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna.bnk |2013-10-15 13:23:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa |2013-10-15 13:23:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa |2013-10-15 13:23:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa.bnk |2013-10-15 13:23:09| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa.bnk |2013-10-15 13:23:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg |2013-10-15 13:23:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg |2013-10-15 13:23:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map |2013-10-15 13:23:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map |2013-10-15 13:23:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.faa |2013-10-15 13:23:10| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.41.asm.contig |2013-10-15 13:23:10| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:23:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka --prefix mira.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.41.asm.contig |2013-10-15 13:23:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka/mira.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.fna |2013-10-15 13:23:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka/mira.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.faa |2013-10-15 13:23:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.gene.cvg |2013-10-15 13:23:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.gene.map |2013-10-15 13:23:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna |2013-10-15 13:23:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna |2013-10-15 13:23:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna.bnk |2013-10-15 13:23:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna.bnk |2013-10-15 13:23:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa |2013-10-15 13:23:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa |2013-10-15 13:23:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa.bnk |2013-10-15 13:23:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa.bnk |2013-10-15 13:23:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg |2013-10-15 13:23:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg |2013-10-15 13:23:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map |2013-10-15 13:23:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map |2013-10-15 13:23:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.faa |2013-10-15 13:23:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.45.asm.contig |2013-10-15 13:23:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:24:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka --prefix mira.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.45.asm.contig |2013-10-15 13:24:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka/mira.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.fna |2013-10-15 13:24:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka/mira.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.faa |2013-10-15 13:24:41| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.gene.cvg |2013-10-15 13:24:41| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.gene.map |2013-10-15 13:24:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna |2013-10-15 13:24:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna |2013-10-15 13:24:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna.bnk |2013-10-15 13:24:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna.bnk |2013-10-15 13:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa |2013-10-15 13:24:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa |2013-10-15 13:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa.bnk |2013-10-15 13:24:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa.bnk |2013-10-15 13:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg |2013-10-15 13:24:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg |2013-10-15 13:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map |2013-10-15 13:24:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map |2013-10-15 13:24:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.faa |2013-10-15 13:24:42| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.55.asm.contig |2013-10-15 13:24:42| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:25:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka --prefix mira.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.55.asm.contig |2013-10-15 13:25:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka/mira.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.fna |2013-10-15 13:25:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka/mira.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.faa |2013-10-15 13:25:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.gene.cvg |2013-10-15 13:25:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.gene.map |2013-10-15 13:25:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna |2013-10-15 13:25:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna |2013-10-15 13:25:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna.bnk |2013-10-15 13:25:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna.bnk |2013-10-15 13:25:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa |2013-10-15 13:25:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa |2013-10-15 13:25:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa.bnk |2013-10-15 13:25:30| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa.bnk |2013-10-15 13:25:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg |2013-10-15 13:25:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg |2013-10-15 13:25:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map |2013-10-15 13:25:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map |2013-10-15 13:25:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.faa |2013-10-15 13:25:31| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.65.asm.contig |2013-10-15 13:25:31| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:26:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka --prefix mira.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.65.asm.contig |2013-10-15 13:26:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka/mira.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.fna |2013-10-15 13:26:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka/mira.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.faa |2013-10-15 13:26:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.gene.cvg |2013-10-15 13:26:16| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.gene.map |2013-10-15 13:26:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna |2013-10-15 13:26:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna |2013-10-15 13:26:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna.bnk |2013-10-15 13:26:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna.bnk |2013-10-15 13:26:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa |2013-10-15 13:26:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa |2013-10-15 13:26:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa.bnk |2013-10-15 13:26:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa.bnk |2013-10-15 13:26:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg |2013-10-15 13:26:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg |2013-10-15 13:26:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map |2013-10-15 13:26:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map |2013-10-15 13:26:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.faa |2013-10-15 13:26:17| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.75.asm.contig |2013-10-15 13:26:17| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:27:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka --prefix mira.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.75.asm.contig |2013-10-15 13:27:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka/mira.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.fna |2013-10-15 13:27:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka/mira.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.faa |2013-10-15 13:27:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.gene.cvg |2013-10-15 13:27:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.gene.map |2013-10-15 13:27:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna |2013-10-15 13:27:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna |2013-10-15 13:27:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna.bnk |2013-10-15 13:27:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna.bnk |2013-10-15 13:27:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa |2013-10-15 13:27:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa |2013-10-15 13:27:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa.bnk |2013-10-15 13:27:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa.bnk |2013-10-15 13:27:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg |2013-10-15 13:27:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg |2013-10-15 13:27:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map |2013-10-15 13:27:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map |2013-10-15 13:27:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.faa |2013-10-15 13:27:03| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.85.asm.contig |2013-10-15 13:27:03| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:27:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka --prefix mira.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.85.asm.contig |2013-10-15 13:27:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka/mira.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.fna |2013-10-15 13:27:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka/mira.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.faa |2013-10-15 13:27:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.gene.cvg |2013-10-15 13:27:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.gene.map |2013-10-15 13:27:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna |2013-10-15 13:27:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna |2013-10-15 13:27:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna.bnk |2013-10-15 13:27:51| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna.bnk |2013-10-15 13:27:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa |2013-10-15 13:27:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa |2013-10-15 13:27:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa.bnk |2013-10-15 13:27:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa.bnk |2013-10-15 13:27:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg |2013-10-15 13:27:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg |2013-10-15 13:27:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map |2013-10-15 13:27:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map |2013-10-15 13:27:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.faa |2013-10-15 13:27:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.95.asm.contig |2013-10-15 13:27:52| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:28:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka --prefix mira.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.95.asm.contig |2013-10-15 13:28:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka/mira.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.fna |2013-10-15 13:28:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka/mira.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.faa |2013-10-15 13:28:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.gene.cvg |2013-10-15 13:28:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.gene.map |2013-10-15 13:28:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna |2013-10-15 13:28:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna |2013-10-15 13:28:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna.bnk |2013-10-15 13:28:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna.bnk |2013-10-15 13:28:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa |2013-10-15 13:28:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa |2013-10-15 13:28:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa.bnk |2013-10-15 13:28:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa.bnk |2013-10-15 13:28:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg |2013-10-15 13:28:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg |2013-10-15 13:28:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map |2013-10-15 13:28:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map |2013-10-15 13:28:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.faa |2013-10-15 13:28:40| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.105.asm.contig |2013-10-15 13:28:40| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:29:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka --prefix ray.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.105.asm.contig |2013-10-15 13:29:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka/ray.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.fna |2013-10-15 13:29:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka/ray.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.faa |2013-10-15 13:29:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.gene.cvg |2013-10-15 13:29:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.gene.map |2013-10-15 13:29:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna |2013-10-15 13:29:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna |2013-10-15 13:29:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna.bnk |2013-10-15 13:29:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna.bnk |2013-10-15 13:29:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa |2013-10-15 13:29:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa |2013-10-15 13:29:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa.bnk |2013-10-15 13:29:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa.bnk |2013-10-15 13:29:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg |2013-10-15 13:29:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg |2013-10-15 13:29:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map |2013-10-15 13:29:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map |2013-10-15 13:29:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.faa |2013-10-15 13:29:18| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.125.asm.contig |2013-10-15 13:29:18| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 13:29:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka --prefix ray.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.125.asm.contig |2013-10-15 13:29:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka/ray.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.fna |2013-10-15 13:29:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka/ray.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.faa |2013-10-15 13:29:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.gene.cvg |2013-10-15 13:29:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.gene.map |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna |2013-10-15 13:29:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna.bnk |2013-10-15 13:29:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna.bnk |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa |2013-10-15 13:29:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa.bnk |2013-10-15 13:29:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa.bnk |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg |2013-10-15 13:29:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg |2013-10-15 13:29:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map |2013-10-15 13:29:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map |2013-10-15 13:29:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.faa |2013-10-15 13:29:36| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-15 13:29:36| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:32:18|# [FINDORFS] |2013-10-15 14:32:19| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-15 14:32:19| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:37:59|# [FINDORFS] |2013-10-15 14:37:59| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-15 14:37:59| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:40:59|# [FINDORFS] |2013-10-15 14:40:59| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-15 14:40:59| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:41:56|# [MAPREADS] |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.contig.cvg |2013-10-15 14:41:56| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.contig.cvg |2013-10-15 14:41:57| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.contig.cvg |2013-10-15 14:41:58| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.contig.cvg |2013-10-15 14:41:59|# [FINDORFS] |2013-10-15 14:41:59| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.25.asm.contig |2013-10-15 14:41:59| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:42:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka --prefix abyss.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.25.asm.contig |2013-10-15 14:42:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka/abyss.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.fna |2013-10-15 14:42:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.prokka/abyss.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.faa |2013-10-15 14:42:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.gene.cvg |2013-10-15 14:42:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.ctg.gene.map |2013-10-15 14:42:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna |2013-10-15 14:42:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna |2013-10-15 14:42:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna.bnk |2013-10-15 14:42:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna.bnk |2013-10-15 14:42:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa |2013-10-15 14:42:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa |2013-10-15 14:42:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa.bnk |2013-10-15 14:42:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa.bnk |2013-10-15 14:42:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg |2013-10-15 14:42:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.cvg |2013-10-15 14:42:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map |2013-10-15 14:42:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.gene.map |2013-10-15 14:42:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.faa |2013-10-15 14:42:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.fna |2013-10-15 14:42:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.35.asm.contig |2013-10-15 14:42:46| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:43:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka --prefix abyss.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.35.asm.contig |2013-10-15 14:43:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka/abyss.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.fna |2013-10-15 14:43:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.prokka/abyss.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.faa |2013-10-15 14:43:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.gene.cvg |2013-10-15 14:43:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.ctg.gene.map |2013-10-15 14:43:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna |2013-10-15 14:43:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna |2013-10-15 14:43:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna.bnk |2013-10-15 14:43:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna.bnk |2013-10-15 14:43:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa |2013-10-15 14:43:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa |2013-10-15 14:43:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa.bnk |2013-10-15 14:43:30| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa.bnk |2013-10-15 14:43:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg |2013-10-15 14:43:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.cvg |2013-10-15 14:43:30| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map |2013-10-15 14:43:30| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.gene.map |2013-10-15 14:43:30| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.faa |2013-10-15 14:43:30| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.fna |2013-10-15 14:43:30| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.41.asm.contig |2013-10-15 14:43:30| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:44:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka --prefix abyss.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.41.asm.contig |2013-10-15 14:44:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka/abyss.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.fna |2013-10-15 14:44:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.prokka/abyss.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.faa |2013-10-15 14:44:11| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.gene.cvg |2013-10-15 14:44:11| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.ctg.gene.map |2013-10-15 14:44:11| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna |2013-10-15 14:44:11| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna |2013-10-15 14:44:11| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna.bnk |2013-10-15 14:44:12| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna.bnk |2013-10-15 14:44:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa |2013-10-15 14:44:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa |2013-10-15 14:44:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa.bnk |2013-10-15 14:44:12| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa.bnk |2013-10-15 14:44:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg |2013-10-15 14:44:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.cvg |2013-10-15 14:44:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map |2013-10-15 14:44:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.gene.map |2013-10-15 14:44:12| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.faa |2013-10-15 14:44:12| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.fna |2013-10-15 14:44:12| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.45.asm.contig |2013-10-15 14:44:12| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:44:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka --prefix abyss.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.45.asm.contig |2013-10-15 14:44:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka/abyss.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.fna |2013-10-15 14:44:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.prokka/abyss.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.faa |2013-10-15 14:44:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.gene.cvg |2013-10-15 14:44:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.ctg.gene.map |2013-10-15 14:44:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna |2013-10-15 14:44:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna |2013-10-15 14:44:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna.bnk |2013-10-15 14:44:54| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna.bnk |2013-10-15 14:44:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa |2013-10-15 14:44:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa |2013-10-15 14:44:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa.bnk |2013-10-15 14:44:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa.bnk |2013-10-15 14:44:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg |2013-10-15 14:44:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.cvg |2013-10-15 14:44:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map |2013-10-15 14:44:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.gene.map |2013-10-15 14:44:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.faa |2013-10-15 14:44:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.fna |2013-10-15 14:44:55| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.55.asm.contig |2013-10-15 14:44:55| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:45:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka --prefix abyss.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.55.asm.contig |2013-10-15 14:45:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka/abyss.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.fna |2013-10-15 14:45:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.prokka/abyss.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.faa |2013-10-15 14:45:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.gene.cvg |2013-10-15 14:45:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.ctg.gene.map |2013-10-15 14:45:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna |2013-10-15 14:45:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna |2013-10-15 14:45:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna.bnk |2013-10-15 14:45:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna.bnk |2013-10-15 14:45:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa |2013-10-15 14:45:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa |2013-10-15 14:45:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa.bnk |2013-10-15 14:45:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa.bnk |2013-10-15 14:45:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg |2013-10-15 14:45:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.cvg |2013-10-15 14:45:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map |2013-10-15 14:45:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.gene.map |2013-10-15 14:45:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.faa |2013-10-15 14:45:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.fna |2013-10-15 14:45:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.65.asm.contig |2013-10-15 14:45:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:46:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka --prefix abyss.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.65.asm.contig |2013-10-15 14:46:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka/abyss.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.fna |2013-10-15 14:46:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.prokka/abyss.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.faa |2013-10-15 14:46:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.gene.cvg |2013-10-15 14:46:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.ctg.gene.map |2013-10-15 14:46:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna |2013-10-15 14:46:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna |2013-10-15 14:46:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna.bnk |2013-10-15 14:46:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna.bnk |2013-10-15 14:46:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa |2013-10-15 14:46:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa |2013-10-15 14:46:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa.bnk |2013-10-15 14:46:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa.bnk |2013-10-15 14:46:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg |2013-10-15 14:46:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.cvg |2013-10-15 14:46:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map |2013-10-15 14:46:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.gene.map |2013-10-15 14:46:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.faa |2013-10-15 14:46:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.fna |2013-10-15 14:46:19| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.75.asm.contig |2013-10-15 14:46:19| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:46:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka --prefix abyss.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.75.asm.contig |2013-10-15 14:46:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka/abyss.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.fna |2013-10-15 14:46:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.prokka/abyss.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.faa |2013-10-15 14:46:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.gene.cvg |2013-10-15 14:46:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.ctg.gene.map |2013-10-15 14:46:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna |2013-10-15 14:46:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna |2013-10-15 14:46:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna.bnk |2013-10-15 14:46:59| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna.bnk |2013-10-15 14:46:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa |2013-10-15 14:46:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa |2013-10-15 14:46:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa.bnk |2013-10-15 14:47:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa.bnk |2013-10-15 14:47:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg |2013-10-15 14:47:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.cvg |2013-10-15 14:47:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map |2013-10-15 14:47:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.gene.map |2013-10-15 14:47:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.faa |2013-10-15 14:47:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.fna |2013-10-15 14:47:00| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.85.asm.contig |2013-10-15 14:47:00| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:47:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka --prefix abyss.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.85.asm.contig |2013-10-15 14:47:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka/abyss.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.fna |2013-10-15 14:47:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.prokka/abyss.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.faa |2013-10-15 14:47:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.gene.cvg |2013-10-15 14:47:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.ctg.gene.map |2013-10-15 14:47:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna |2013-10-15 14:47:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna |2013-10-15 14:47:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna.bnk |2013-10-15 14:47:40| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna.bnk |2013-10-15 14:47:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa |2013-10-15 14:47:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa |2013-10-15 14:47:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa.bnk |2013-10-15 14:47:40| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa.bnk |2013-10-15 14:47:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg |2013-10-15 14:47:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.cvg |2013-10-15 14:47:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map |2013-10-15 14:47:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.gene.map |2013-10-15 14:47:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.faa |2013-10-15 14:47:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.fna |2013-10-15 14:47:41| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.95.asm.contig |2013-10-15 14:47:41| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:48:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka --prefix abyss.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/abyss.95.asm.contig |2013-10-15 14:48:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka/abyss.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.fna |2013-10-15 14:48:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.prokka/abyss.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.faa |2013-10-15 14:48:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.gene.cvg |2013-10-15 14:48:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.ctg.gene.map |2013-10-15 14:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna |2013-10-15 14:48:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna |2013-10-15 14:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna.bnk |2013-10-15 14:48:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna.bnk |2013-10-15 14:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa |2013-10-15 14:48:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa |2013-10-15 14:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa.bnk |2013-10-15 14:48:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa.bnk |2013-10-15 14:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg |2013-10-15 14:48:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.cvg |2013-10-15 14:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map |2013-10-15 14:48:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.gene.map |2013-10-15 14:48:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.faa |2013-10-15 14:48:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/abyss.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.fna |2013-10-15 14:48:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.105.asm.contig |2013-10-15 14:48:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:49:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka --prefix idba-ud.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.105.asm.contig |2013-10-15 14:49:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka/idba-ud.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.fna |2013-10-15 14:49:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.prokka/idba-ud.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.faa |2013-10-15 14:49:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.gene.cvg |2013-10-15 14:49:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.ctg.gene.map |2013-10-15 14:49:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna |2013-10-15 14:49:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna |2013-10-15 14:49:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna.bnk |2013-10-15 14:49:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna.bnk |2013-10-15 14:49:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa |2013-10-15 14:49:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa |2013-10-15 14:49:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa.bnk |2013-10-15 14:49:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa.bnk |2013-10-15 14:49:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg |2013-10-15 14:49:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.cvg |2013-10-15 14:49:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map |2013-10-15 14:49:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.gene.map |2013-10-15 14:49:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.faa |2013-10-15 14:49:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.fna |2013-10-15 14:49:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.25.asm.contig |2013-10-15 14:49:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:50:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka --prefix idba-ud.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.25.asm.contig |2013-10-15 14:50:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka/idba-ud.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.fna |2013-10-15 14:50:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.prokka/idba-ud.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.faa |2013-10-15 14:50:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.gene.cvg |2013-10-15 14:50:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.ctg.gene.map |2013-10-15 14:51:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna |2013-10-15 14:51:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna |2013-10-15 14:51:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna.bnk |2013-10-15 14:51:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna.bnk |2013-10-15 14:51:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa |2013-10-15 14:51:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa |2013-10-15 14:51:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa.bnk |2013-10-15 14:51:01| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa.bnk |2013-10-15 14:51:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg |2013-10-15 14:51:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.cvg |2013-10-15 14:51:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map |2013-10-15 14:51:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.gene.map |2013-10-15 14:51:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.faa |2013-10-15 14:51:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.fna |2013-10-15 14:51:01| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.35.asm.contig |2013-10-15 14:51:01| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:52:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka --prefix idba-ud.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.35.asm.contig |2013-10-15 14:52:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka/idba-ud.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.fna |2013-10-15 14:52:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.prokka/idba-ud.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.faa |2013-10-15 14:52:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.gene.cvg |2013-10-15 14:52:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.ctg.gene.map |2013-10-15 14:52:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna |2013-10-15 14:52:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna |2013-10-15 14:52:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna.bnk |2013-10-15 14:52:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna.bnk |2013-10-15 14:52:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa |2013-10-15 14:52:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa |2013-10-15 14:52:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa.bnk |2013-10-15 14:52:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa.bnk |2013-10-15 14:52:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg |2013-10-15 14:52:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.cvg |2013-10-15 14:52:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map |2013-10-15 14:52:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.gene.map |2013-10-15 14:52:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.faa |2013-10-15 14:52:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.fna |2013-10-15 14:52:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.41.asm.contig |2013-10-15 14:52:39| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:54:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka --prefix idba-ud.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.41.asm.contig |2013-10-15 14:54:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka/idba-ud.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.fna |2013-10-15 14:54:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.prokka/idba-ud.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.faa |2013-10-15 14:54:18| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.gene.cvg |2013-10-15 14:54:18| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.ctg.gene.map |2013-10-15 14:54:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna |2013-10-15 14:54:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna |2013-10-15 14:54:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna.bnk |2013-10-15 14:54:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna.bnk |2013-10-15 14:54:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa |2013-10-15 14:54:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa |2013-10-15 14:54:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa.bnk |2013-10-15 14:54:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa.bnk |2013-10-15 14:54:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg |2013-10-15 14:54:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.cvg |2013-10-15 14:54:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map |2013-10-15 14:54:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.gene.map |2013-10-15 14:54:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.faa |2013-10-15 14:54:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.fna |2013-10-15 14:54:20| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.45.asm.contig |2013-10-15 14:54:20| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:56:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka --prefix idba-ud.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.45.asm.contig |2013-10-15 14:56:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka/idba-ud.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.fna |2013-10-15 14:56:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.prokka/idba-ud.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.faa |2013-10-15 14:56:14| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.gene.cvg |2013-10-15 14:56:14| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.ctg.gene.map |2013-10-15 14:56:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna |2013-10-15 14:56:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna |2013-10-15 14:56:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna.bnk |2013-10-15 14:56:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna.bnk |2013-10-15 14:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa |2013-10-15 14:56:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa |2013-10-15 14:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa.bnk |2013-10-15 14:56:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa.bnk |2013-10-15 14:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg |2013-10-15 14:56:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.cvg |2013-10-15 14:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map |2013-10-15 14:56:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.gene.map |2013-10-15 14:56:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.faa |2013-10-15 14:56:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.fna |2013-10-15 14:56:16| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.55.asm.contig |2013-10-15 14:56:16| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:57:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka --prefix idba-ud.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.55.asm.contig |2013-10-15 14:57:26| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka/idba-ud.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.fna |2013-10-15 14:57:26| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.prokka/idba-ud.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.faa |2013-10-15 14:57:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.gene.cvg |2013-10-15 14:57:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.ctg.gene.map |2013-10-15 14:57:26| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna |2013-10-15 14:57:26| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna |2013-10-15 14:57:26| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna.bnk |2013-10-15 14:57:27| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna.bnk |2013-10-15 14:57:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa |2013-10-15 14:57:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa |2013-10-15 14:57:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa.bnk |2013-10-15 14:57:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa.bnk |2013-10-15 14:57:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg |2013-10-15 14:57:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.cvg |2013-10-15 14:57:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map |2013-10-15 14:57:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.gene.map |2013-10-15 14:57:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.faa |2013-10-15 14:57:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.fna |2013-10-15 14:57:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.65.asm.contig |2013-10-15 14:57:30| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:58:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka --prefix idba-ud.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.65.asm.contig |2013-10-15 14:58:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka/idba-ud.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.fna |2013-10-15 14:58:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.prokka/idba-ud.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.faa |2013-10-15 14:58:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.gene.cvg |2013-10-15 14:58:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.ctg.gene.map |2013-10-15 14:58:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna |2013-10-15 14:58:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna |2013-10-15 14:58:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna.bnk |2013-10-15 14:58:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna.bnk |2013-10-15 14:58:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa |2013-10-15 14:58:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa |2013-10-15 14:58:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa.bnk |2013-10-15 14:58:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa.bnk |2013-10-15 14:58:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg |2013-10-15 14:58:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.cvg |2013-10-15 14:58:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map |2013-10-15 14:58:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.gene.map |2013-10-15 14:58:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.faa |2013-10-15 14:58:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.fna |2013-10-15 14:58:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.75.asm.contig |2013-10-15 14:58:43| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 14:59:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka --prefix idba-ud.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.75.asm.contig |2013-10-15 14:59:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka/idba-ud.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.fna |2013-10-15 14:59:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.prokka/idba-ud.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.faa |2013-10-15 14:59:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.gene.cvg |2013-10-15 14:59:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.ctg.gene.map |2013-10-15 14:59:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna |2013-10-15 14:59:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna |2013-10-15 14:59:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna.bnk |2013-10-15 14:59:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna.bnk |2013-10-15 14:59:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa |2013-10-15 14:59:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa |2013-10-15 14:59:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa.bnk |2013-10-15 14:59:53| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa.bnk |2013-10-15 14:59:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg |2013-10-15 14:59:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.cvg |2013-10-15 14:59:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map |2013-10-15 14:59:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.gene.map |2013-10-15 14:59:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.faa |2013-10-15 14:59:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.fna |2013-10-15 14:59:53| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.85.asm.contig |2013-10-15 14:59:53| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:00:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka --prefix idba-ud.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.85.asm.contig |2013-10-15 15:00:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka/idba-ud.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.fna |2013-10-15 15:00:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.prokka/idba-ud.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.faa |2013-10-15 15:00:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.gene.cvg |2013-10-15 15:00:58| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.ctg.gene.map |2013-10-15 15:00:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna |2013-10-15 15:00:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna |2013-10-15 15:00:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna.bnk |2013-10-15 15:00:59| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna.bnk |2013-10-15 15:00:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa |2013-10-15 15:00:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa |2013-10-15 15:00:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa.bnk |2013-10-15 15:00:59| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa.bnk |2013-10-15 15:01:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg |2013-10-15 15:01:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.cvg |2013-10-15 15:01:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map |2013-10-15 15:01:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.gene.map |2013-10-15 15:01:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.faa |2013-10-15 15:01:00| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.fna |2013-10-15 15:01:00| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.95.asm.contig |2013-10-15 15:01:00| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:01:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka --prefix idba-ud.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/idba-ud.95.asm.contig |2013-10-15 15:01:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka/idba-ud.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.fna |2013-10-15 15:01:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.prokka/idba-ud.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.faa |2013-10-15 15:01:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.gene.cvg |2013-10-15 15:01:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.ctg.gene.map |2013-10-15 15:01:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna |2013-10-15 15:02:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna |2013-10-15 15:02:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna.bnk |2013-10-15 15:02:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna.bnk |2013-10-15 15:02:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa |2013-10-15 15:02:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa |2013-10-15 15:02:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa.bnk |2013-10-15 15:02:01| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa.bnk |2013-10-15 15:02:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg |2013-10-15 15:02:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.cvg |2013-10-15 15:02:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map |2013-10-15 15:02:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.gene.map |2013-10-15 15:02:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.faa |2013-10-15 15:02:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/idba-ud.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.fna |2013-10-15 15:02:01| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-10-15 15:02:01| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:02:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka --prefix masurca.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-10-15 15:02:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka/masurca.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.fna |2013-10-15 15:02:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.prokka/masurca.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.faa |2013-10-15 15:02:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.gene.cvg |2013-10-15 15:02:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.ctg.gene.map |2013-10-15 15:02:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna |2013-10-15 15:02:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna |2013-10-15 15:02:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna.bnk |2013-10-15 15:02:47| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna.bnk |2013-10-15 15:02:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa |2013-10-15 15:02:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa |2013-10-15 15:02:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa.bnk |2013-10-15 15:02:47| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa.bnk |2013-10-15 15:02:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg |2013-10-15 15:02:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.cvg |2013-10-15 15:02:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map |2013-10-15 15:02:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.gene.map |2013-10-15 15:02:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.faa |2013-10-15 15:02:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.fna |2013-10-15 15:02:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.125.asm.contig |2013-10-15 15:02:47| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:03:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka --prefix masurca.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.125.asm.contig |2013-10-15 15:03:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka/masurca.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.fna |2013-10-15 15:03:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.prokka/masurca.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.faa |2013-10-15 15:03:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.gene.cvg |2013-10-15 15:03:27| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.ctg.gene.map |2013-10-15 15:03:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna |2013-10-15 15:03:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna |2013-10-15 15:03:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna.bnk |2013-10-15 15:03:28| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna.bnk |2013-10-15 15:03:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa |2013-10-15 15:03:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa |2013-10-15 15:03:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa.bnk |2013-10-15 15:03:28| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa.bnk |2013-10-15 15:03:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg |2013-10-15 15:03:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.cvg |2013-10-15 15:03:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map |2013-10-15 15:03:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.gene.map |2013-10-15 15:03:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.faa |2013-10-15 15:03:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.fna |2013-10-15 15:03:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.25.asm.contig |2013-10-15 15:03:29| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:04:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka --prefix masurca.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.25.asm.contig |2013-10-15 15:04:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka/masurca.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.fna |2013-10-15 15:04:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.prokka/masurca.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.faa |2013-10-15 15:04:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.gene.cvg |2013-10-15 15:04:17| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.ctg.gene.map |2013-10-15 15:04:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna |2013-10-15 15:04:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna |2013-10-15 15:04:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna.bnk |2013-10-15 15:04:18| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna.bnk |2013-10-15 15:04:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa |2013-10-15 15:04:18| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa |2013-10-15 15:04:18| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa.bnk |2013-10-15 15:04:19| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa.bnk |2013-10-15 15:04:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg |2013-10-15 15:04:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.cvg |2013-10-15 15:04:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map |2013-10-15 15:04:19| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.gene.map |2013-10-15 15:04:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.faa |2013-10-15 15:04:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.fna |2013-10-15 15:04:19| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.35.asm.contig |2013-10-15 15:04:19| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:05:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka --prefix masurca.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.35.asm.contig |2013-10-15 15:05:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka/masurca.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.fna |2013-10-15 15:05:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.prokka/masurca.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.faa |2013-10-15 15:05:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.gene.cvg |2013-10-15 15:05:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.ctg.gene.map |2013-10-15 15:05:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna |2013-10-15 15:05:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna |2013-10-15 15:05:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna.bnk |2013-10-15 15:05:04| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna.bnk |2013-10-15 15:05:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa |2013-10-15 15:05:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa |2013-10-15 15:05:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa.bnk |2013-10-15 15:05:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa.bnk |2013-10-15 15:05:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg |2013-10-15 15:05:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.cvg |2013-10-15 15:05:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map |2013-10-15 15:05:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.gene.map |2013-10-15 15:05:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.faa |2013-10-15 15:05:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.fna |2013-10-15 15:05:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.41.asm.contig |2013-10-15 15:05:06| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:05:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka --prefix masurca.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.41.asm.contig |2013-10-15 15:05:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka/masurca.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.fna |2013-10-15 15:05:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.prokka/masurca.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.faa |2013-10-15 15:05:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.gene.cvg |2013-10-15 15:05:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.ctg.gene.map |2013-10-15 15:05:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna |2013-10-15 15:05:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna |2013-10-15 15:05:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna.bnk |2013-10-15 15:05:51| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna.bnk |2013-10-15 15:05:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa |2013-10-15 15:05:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa |2013-10-15 15:05:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa.bnk |2013-10-15 15:05:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa.bnk |2013-10-15 15:05:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg |2013-10-15 15:05:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.cvg |2013-10-15 15:05:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map |2013-10-15 15:05:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.gene.map |2013-10-15 15:05:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.faa |2013-10-15 15:05:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.fna |2013-10-15 15:05:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.45.asm.contig |2013-10-15 15:05:52| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:06:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka --prefix masurca.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.45.asm.contig |2013-10-15 15:06:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka/masurca.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.fna |2013-10-15 15:06:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.prokka/masurca.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.faa |2013-10-15 15:06:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.gene.cvg |2013-10-15 15:06:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.ctg.gene.map |2013-10-15 15:06:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna |2013-10-15 15:06:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna |2013-10-15 15:06:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna.bnk |2013-10-15 15:06:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna.bnk |2013-10-15 15:06:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa |2013-10-15 15:06:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa |2013-10-15 15:06:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa.bnk |2013-10-15 15:06:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa.bnk |2013-10-15 15:06:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg |2013-10-15 15:06:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.cvg |2013-10-15 15:06:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map |2013-10-15 15:06:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.gene.map |2013-10-15 15:06:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.faa |2013-10-15 15:06:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.fna |2013-10-15 15:06:38| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.55.asm.contig |2013-10-15 15:06:38| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:07:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka --prefix masurca.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.55.asm.contig |2013-10-15 15:07:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka/masurca.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.fna |2013-10-15 15:07:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.prokka/masurca.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.faa |2013-10-15 15:07:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.gene.cvg |2013-10-15 15:07:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.ctg.gene.map |2013-10-15 15:07:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna |2013-10-15 15:07:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna |2013-10-15 15:07:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna.bnk |2013-10-15 15:07:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna.bnk |2013-10-15 15:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa |2013-10-15 15:07:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa |2013-10-15 15:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa.bnk |2013-10-15 15:07:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa.bnk |2013-10-15 15:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg |2013-10-15 15:07:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.cvg |2013-10-15 15:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map |2013-10-15 15:07:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.gene.map |2013-10-15 15:07:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.faa |2013-10-15 15:07:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.fna |2013-10-15 15:07:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.65.asm.contig |2013-10-15 15:07:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:08:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka --prefix masurca.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.65.asm.contig |2013-10-15 15:08:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka/masurca.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.fna |2013-10-15 15:08:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.prokka/masurca.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.faa |2013-10-15 15:08:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.gene.cvg |2013-10-15 15:08:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.ctg.gene.map |2013-10-15 15:08:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna |2013-10-15 15:08:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna |2013-10-15 15:08:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna.bnk |2013-10-15 15:08:04| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna.bnk |2013-10-15 15:08:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa |2013-10-15 15:08:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa |2013-10-15 15:08:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa.bnk |2013-10-15 15:08:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa.bnk |2013-10-15 15:08:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg |2013-10-15 15:08:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.cvg |2013-10-15 15:08:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map |2013-10-15 15:08:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.gene.map |2013-10-15 15:08:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.faa |2013-10-15 15:08:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.fna |2013-10-15 15:08:05| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.75.asm.contig |2013-10-15 15:08:05| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:08:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka --prefix masurca.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.75.asm.contig |2013-10-15 15:08:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka/masurca.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.fna |2013-10-15 15:08:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.prokka/masurca.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.faa |2013-10-15 15:08:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.gene.cvg |2013-10-15 15:08:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.ctg.gene.map |2013-10-15 15:08:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna |2013-10-15 15:08:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna |2013-10-15 15:08:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna.bnk |2013-10-15 15:08:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna.bnk |2013-10-15 15:08:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa |2013-10-15 15:08:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa |2013-10-15 15:08:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa.bnk |2013-10-15 15:08:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa.bnk |2013-10-15 15:08:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg |2013-10-15 15:08:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.cvg |2013-10-15 15:08:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map |2013-10-15 15:08:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.gene.map |2013-10-15 15:08:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.faa |2013-10-15 15:08:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.fna |2013-10-15 15:08:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.85.asm.contig |2013-10-15 15:08:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:09:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka --prefix masurca.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.85.asm.contig |2013-10-15 15:09:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka/masurca.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.fna |2013-10-15 15:09:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.prokka/masurca.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.faa |2013-10-15 15:09:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.gene.cvg |2013-10-15 15:09:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.ctg.gene.map |2013-10-15 15:09:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna |2013-10-15 15:09:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna |2013-10-15 15:09:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna.bnk |2013-10-15 15:09:48| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna.bnk |2013-10-15 15:09:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa |2013-10-15 15:09:48| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa |2013-10-15 15:09:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa.bnk |2013-10-15 15:09:49| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa.bnk |2013-10-15 15:09:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg |2013-10-15 15:09:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.cvg |2013-10-15 15:09:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map |2013-10-15 15:09:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.gene.map |2013-10-15 15:09:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.faa |2013-10-15 15:09:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.fna |2013-10-15 15:09:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.95.asm.contig |2013-10-15 15:09:50| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:10:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka --prefix masurca.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.95.asm.contig |2013-10-15 15:10:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka/masurca.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.fna |2013-10-15 15:10:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.prokka/masurca.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.faa |2013-10-15 15:10:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.gene.cvg |2013-10-15 15:10:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.ctg.gene.map |2013-10-15 15:10:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna |2013-10-15 15:10:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna |2013-10-15 15:10:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna.bnk |2013-10-15 15:10:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna.bnk |2013-10-15 15:10:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa |2013-10-15 15:10:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa |2013-10-15 15:10:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa.bnk |2013-10-15 15:10:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa.bnk |2013-10-15 15:10:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg |2013-10-15 15:10:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.cvg |2013-10-15 15:10:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map |2013-10-15 15:10:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.gene.map |2013-10-15 15:10:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.faa |2013-10-15 15:10:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/masurca.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.fna |2013-10-15 15:10:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.105.asm.contig |2013-10-15 15:10:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:11:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka --prefix mira.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.105.asm.contig |2013-10-15 15:11:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka/mira.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.fna |2013-10-15 15:11:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.prokka/mira.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.faa |2013-10-15 15:11:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.gene.cvg |2013-10-15 15:11:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.ctg.gene.map |2013-10-15 15:11:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna |2013-10-15 15:11:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna |2013-10-15 15:11:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna.bnk |2013-10-15 15:11:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna.bnk |2013-10-15 15:11:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa |2013-10-15 15:11:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa |2013-10-15 15:11:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa.bnk |2013-10-15 15:11:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa.bnk |2013-10-15 15:11:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg |2013-10-15 15:11:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.cvg |2013-10-15 15:11:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map |2013-10-15 15:11:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.gene.map |2013-10-15 15:11:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.faa |2013-10-15 15:11:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.fna |2013-10-15 15:11:23| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.125.asm.contig |2013-10-15 15:11:23| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:12:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka --prefix mira.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.125.asm.contig |2013-10-15 15:12:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka/mira.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.fna |2013-10-15 15:12:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.prokka/mira.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.faa |2013-10-15 15:12:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.gene.cvg |2013-10-15 15:12:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.ctg.gene.map |2013-10-15 15:12:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna |2013-10-15 15:12:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna |2013-10-15 15:12:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna.bnk |2013-10-15 15:12:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna.bnk |2013-10-15 15:12:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa |2013-10-15 15:12:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa |2013-10-15 15:12:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa.bnk |2013-10-15 15:12:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa.bnk |2013-10-15 15:12:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg |2013-10-15 15:12:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.cvg |2013-10-15 15:12:17| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map |2013-10-15 15:12:17| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.gene.map |2013-10-15 15:12:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.faa |2013-10-15 15:12:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.fna |2013-10-15 15:12:17| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.25.asm.contig |2013-10-15 15:12:17| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:13:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka --prefix mira.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.25.asm.contig |2013-10-15 15:13:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka/mira.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.fna |2013-10-15 15:13:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.prokka/mira.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.faa |2013-10-15 15:13:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.gene.cvg |2013-10-15 15:13:04| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.ctg.gene.map |2013-10-15 15:13:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna |2013-10-15 15:13:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna |2013-10-15 15:13:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna.bnk |2013-10-15 15:13:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna.bnk |2013-10-15 15:13:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa |2013-10-15 15:13:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa |2013-10-15 15:13:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa.bnk |2013-10-15 15:13:06| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa.bnk |2013-10-15 15:13:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg |2013-10-15 15:13:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.cvg |2013-10-15 15:13:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map |2013-10-15 15:13:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.gene.map |2013-10-15 15:13:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.faa |2013-10-15 15:13:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.fna |2013-10-15 15:13:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.35.asm.contig |2013-10-15 15:13:06| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:14:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka --prefix mira.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.35.asm.contig |2013-10-15 15:14:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka/mira.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.fna |2013-10-15 15:14:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.prokka/mira.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.faa |2013-10-15 15:14:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.gene.cvg |2013-10-15 15:14:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.ctg.gene.map |2013-10-15 15:14:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna |2013-10-15 15:14:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna |2013-10-15 15:14:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna.bnk |2013-10-15 15:14:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna.bnk |2013-10-15 15:14:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa |2013-10-15 15:14:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa |2013-10-15 15:14:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa.bnk |2013-10-15 15:14:03| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa.bnk |2013-10-15 15:14:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg |2013-10-15 15:14:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.cvg |2013-10-15 15:14:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map |2013-10-15 15:14:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.gene.map |2013-10-15 15:14:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.faa |2013-10-15 15:14:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.fna |2013-10-15 15:14:03| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.41.asm.contig |2013-10-15 15:14:03| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:14:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka --prefix mira.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.41.asm.contig |2013-10-15 15:14:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka/mira.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.fna |2013-10-15 15:14:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.prokka/mira.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.faa |2013-10-15 15:14:52| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.gene.cvg |2013-10-15 15:14:52| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.ctg.gene.map |2013-10-15 15:14:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna |2013-10-15 15:14:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna |2013-10-15 15:14:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna.bnk |2013-10-15 15:14:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna.bnk |2013-10-15 15:14:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa |2013-10-15 15:14:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa |2013-10-15 15:14:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa.bnk |2013-10-15 15:14:53| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa.bnk |2013-10-15 15:14:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg |2013-10-15 15:14:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.cvg |2013-10-15 15:14:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map |2013-10-15 15:14:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.gene.map |2013-10-15 15:14:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.faa |2013-10-15 15:14:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.fna |2013-10-15 15:14:53| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.45.asm.contig |2013-10-15 15:14:53| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:15:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka --prefix mira.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.45.asm.contig |2013-10-15 15:15:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka/mira.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.fna |2013-10-15 15:15:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.prokka/mira.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.faa |2013-10-15 15:15:41| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.gene.cvg |2013-10-15 15:15:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.ctg.gene.map |2013-10-15 15:15:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna |2013-10-15 15:15:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna |2013-10-15 15:15:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna.bnk |2013-10-15 15:15:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna.bnk |2013-10-15 15:15:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa |2013-10-15 15:15:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa |2013-10-15 15:15:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa.bnk |2013-10-15 15:15:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa.bnk |2013-10-15 15:15:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg |2013-10-15 15:15:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.cvg |2013-10-15 15:15:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map |2013-10-15 15:15:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.gene.map |2013-10-15 15:15:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.faa |2013-10-15 15:15:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.fna |2013-10-15 15:15:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.55.asm.contig |2013-10-15 15:15:43| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:16:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka --prefix mira.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.55.asm.contig |2013-10-15 15:16:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka/mira.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.fna |2013-10-15 15:16:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.prokka/mira.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.faa |2013-10-15 15:16:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.gene.cvg |2013-10-15 15:16:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.ctg.gene.map |2013-10-15 15:16:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna |2013-10-15 15:16:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna |2013-10-15 15:16:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna.bnk |2013-10-15 15:16:32| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna.bnk |2013-10-15 15:16:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa |2013-10-15 15:16:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa |2013-10-15 15:16:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa.bnk |2013-10-15 15:16:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa.bnk |2013-10-15 15:16:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg |2013-10-15 15:16:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.cvg |2013-10-15 15:16:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map |2013-10-15 15:16:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.gene.map |2013-10-15 15:16:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.faa |2013-10-15 15:16:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.fna |2013-10-15 15:16:33| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.65.asm.contig |2013-10-15 15:16:33| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:17:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka --prefix mira.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.65.asm.contig |2013-10-15 15:17:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka/mira.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.fna |2013-10-15 15:17:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.prokka/mira.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.faa |2013-10-15 15:17:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.gene.cvg |2013-10-15 15:17:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.ctg.gene.map |2013-10-15 15:17:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna |2013-10-15 15:17:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna |2013-10-15 15:17:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna.bnk |2013-10-15 15:17:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna.bnk |2013-10-15 15:17:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa |2013-10-15 15:17:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa |2013-10-15 15:17:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa.bnk |2013-10-15 15:17:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa.bnk |2013-10-15 15:17:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg |2013-10-15 15:17:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.cvg |2013-10-15 15:17:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map |2013-10-15 15:17:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.gene.map |2013-10-15 15:17:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.faa |2013-10-15 15:17:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.fna |2013-10-15 15:17:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.75.asm.contig |2013-10-15 15:17:29| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:18:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka --prefix mira.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.75.asm.contig |2013-10-15 15:18:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka/mira.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.fna |2013-10-15 15:18:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.prokka/mira.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.faa |2013-10-15 15:18:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.gene.cvg |2013-10-15 15:18:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.ctg.gene.map |2013-10-15 15:18:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna |2013-10-15 15:18:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna |2013-10-15 15:18:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna.bnk |2013-10-15 15:18:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna.bnk |2013-10-15 15:18:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa |2013-10-15 15:18:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa |2013-10-15 15:18:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa.bnk |2013-10-15 15:18:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa.bnk |2013-10-15 15:18:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg |2013-10-15 15:18:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.cvg |2013-10-15 15:18:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map |2013-10-15 15:18:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.gene.map |2013-10-15 15:18:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.faa |2013-10-15 15:18:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.fna |2013-10-15 15:18:16| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.85.asm.contig |2013-10-15 15:18:16| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:19:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka --prefix mira.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.85.asm.contig |2013-10-15 15:19:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka/mira.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.fna |2013-10-15 15:19:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.prokka/mira.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.faa |2013-10-15 15:19:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.gene.cvg |2013-10-15 15:19:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.ctg.gene.map |2013-10-15 15:19:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna |2013-10-15 15:19:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna |2013-10-15 15:19:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna.bnk |2013-10-15 15:19:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna.bnk |2013-10-15 15:19:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa |2013-10-15 15:19:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa |2013-10-15 15:19:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa.bnk |2013-10-15 15:19:06| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa.bnk |2013-10-15 15:19:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg |2013-10-15 15:19:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.cvg |2013-10-15 15:19:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map |2013-10-15 15:19:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.gene.map |2013-10-15 15:19:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.faa |2013-10-15 15:19:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.fna |2013-10-15 15:19:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.95.asm.contig |2013-10-15 15:19:06| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:19:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka --prefix mira.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/mira.95.asm.contig |2013-10-15 15:19:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka/mira.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.fna |2013-10-15 15:19:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.prokka/mira.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.faa |2013-10-15 15:19:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.gene.cvg |2013-10-15 15:19:54| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.ctg.gene.map |2013-10-15 15:19:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna |2013-10-15 15:19:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna |2013-10-15 15:19:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna.bnk |2013-10-15 15:19:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna.bnk |2013-10-15 15:19:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa |2013-10-15 15:19:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa |2013-10-15 15:19:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa.bnk |2013-10-15 15:19:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa.bnk |2013-10-15 15:19:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg |2013-10-15 15:19:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.cvg |2013-10-15 15:19:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map |2013-10-15 15:19:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.gene.map |2013-10-15 15:19:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.faa |2013-10-15 15:19:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/mira.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.fna |2013-10-15 15:19:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.105.asm.contig |2013-10-15 15:19:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:20:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka --prefix ray.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.105.asm.contig |2013-10-15 15:20:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka/ray.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.fna |2013-10-15 15:20:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.prokka/ray.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.faa |2013-10-15 15:20:34| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.gene.cvg |2013-10-15 15:20:35| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.ctg.gene.map |2013-10-15 15:20:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna |2013-10-15 15:20:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna |2013-10-15 15:20:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna.bnk |2013-10-15 15:20:35| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna.bnk |2013-10-15 15:20:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa |2013-10-15 15:20:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa |2013-10-15 15:20:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa.bnk |2013-10-15 15:20:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa.bnk |2013-10-15 15:20:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg |2013-10-15 15:20:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.cvg |2013-10-15 15:20:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map |2013-10-15 15:20:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.gene.map |2013-10-15 15:20:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.faa |2013-10-15 15:20:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.fna |2013-10-15 15:20:36| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.125.asm.contig |2013-10-15 15:20:36| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-15 15:20:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka --prefix ray.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.125.asm.contig |2013-10-15 15:20:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka/ray.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.fna |2013-10-15 15:20:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.prokka/ray.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.faa |2013-10-15 15:20:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.gene.cvg |2013-10-15 15:20:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.ctg.gene.map |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna |2013-10-15 15:20:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna.bnk |2013-10-15 15:20:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna.bnk |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa |2013-10-15 15:20:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa.bnk |2013-10-15 15:20:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa.bnk |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg |2013-10-15 15:20:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.cvg |2013-10-15 15:20:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map |2013-10-15 15:20:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.gene.map |2013-10-15 15:20:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.faa |2013-10-15 15:20:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.fna |2013-10-15 15:20:56| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-15 15:20:56| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:45:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.prokka --prefix ray.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.25.asm.contig |2013-10-16 10:45:26| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.prokka/ray.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.ctg.fna |2013-10-16 10:45:26| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.prokka/ray.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.ctg.faa |2013-10-16 10:45:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.ctg.gene.cvg |2013-10-16 10:45:26| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.ctg.gene.map |2013-10-16 10:45:26| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna |2013-10-16 10:45:26| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna |2013-10-16 10:45:26| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna.bnk |2013-10-16 10:45:27| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna.bnk |2013-10-16 10:45:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa |2013-10-16 10:45:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa |2013-10-16 10:45:27| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa.bnk |2013-10-16 10:45:28| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa.bnk |2013-10-16 10:45:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.cvg |2013-10-16 10:45:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.cvg |2013-10-16 10:45:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.map |2013-10-16 10:45:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.gene.map |2013-10-16 10:45:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.faa |2013-10-16 10:45:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.fna |2013-10-16 10:45:28| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.35.asm.contig |2013-10-16 10:45:28| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:55:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.prokka --prefix ray.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.35.asm.contig |2013-10-16 10:55:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.prokka/ray.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.ctg.fna |2013-10-16 10:55:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.prokka/ray.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.ctg.faa |2013-10-16 10:55:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.ctg.gene.cvg |2013-10-16 10:55:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.ctg.gene.map |2013-10-16 10:55:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna |2013-10-16 10:55:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna |2013-10-16 10:55:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna.bnk |2013-10-16 10:55:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna.bnk |2013-10-16 10:55:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa |2013-10-16 10:55:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa |2013-10-16 10:55:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa.bnk |2013-10-16 10:55:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa.bnk |2013-10-16 10:55:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.cvg |2013-10-16 10:55:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.cvg |2013-10-16 10:55:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.map |2013-10-16 10:55:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.gene.map |2013-10-16 10:55:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.faa |2013-10-16 10:55:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.fna |2013-10-16 10:55:24| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.41.asm.contig |2013-10-16 10:55:24| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:56:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.prokka --prefix ray.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.41.asm.contig |2013-10-16 10:56:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.prokka/ray.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.ctg.fna |2013-10-16 10:56:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.prokka/ray.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.ctg.faa |2013-10-16 10:56:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.ctg.gene.cvg |2013-10-16 10:56:22| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.ctg.gene.map |2013-10-16 10:56:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna |2013-10-16 10:56:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna |2013-10-16 10:56:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna.bnk |2013-10-16 10:56:22| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna.bnk |2013-10-16 10:56:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa |2013-10-16 10:56:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa |2013-10-16 10:56:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa.bnk |2013-10-16 10:56:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa.bnk |2013-10-16 10:56:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.cvg |2013-10-16 10:56:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.cvg |2013-10-16 10:56:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.map |2013-10-16 10:56:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.gene.map |2013-10-16 10:56:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.faa |2013-10-16 10:56:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.fna |2013-10-16 10:56:23| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.45.asm.contig |2013-10-16 10:56:23| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:57:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.prokka --prefix ray.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.45.asm.contig |2013-10-16 10:57:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.prokka/ray.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.ctg.fna |2013-10-16 10:57:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.prokka/ray.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.ctg.faa |2013-10-16 10:57:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.ctg.gene.cvg |2013-10-16 10:57:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.ctg.gene.map |2013-10-16 10:57:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna |2013-10-16 10:57:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna |2013-10-16 10:57:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna.bnk |2013-10-16 10:57:08| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna.bnk |2013-10-16 10:57:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa |2013-10-16 10:57:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa |2013-10-16 10:57:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa.bnk |2013-10-16 10:57:09| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa.bnk |2013-10-16 10:57:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.cvg |2013-10-16 10:57:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.cvg |2013-10-16 10:57:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.map |2013-10-16 10:57:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.gene.map |2013-10-16 10:57:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.faa |2013-10-16 10:57:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.fna |2013-10-16 10:57:09| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.55.asm.contig |2013-10-16 10:57:09| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:57:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.prokka --prefix ray.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.55.asm.contig |2013-10-16 10:57:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.prokka/ray.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.ctg.fna |2013-10-16 10:57:51| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.prokka/ray.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.ctg.faa |2013-10-16 10:57:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.ctg.gene.cvg |2013-10-16 10:57:51| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.ctg.gene.map |2013-10-16 10:57:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna |2013-10-16 10:57:51| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna |2013-10-16 10:57:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna.bnk |2013-10-16 10:57:51| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna.bnk |2013-10-16 10:57:51| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa |2013-10-16 10:57:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa |2013-10-16 10:57:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa.bnk |2013-10-16 10:57:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa.bnk |2013-10-16 10:57:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.cvg |2013-10-16 10:57:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.cvg |2013-10-16 10:57:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.map |2013-10-16 10:57:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.gene.map |2013-10-16 10:57:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.faa |2013-10-16 10:57:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.fna |2013-10-16 10:57:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.65.asm.contig |2013-10-16 10:57:52| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:58:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.prokka --prefix ray.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.65.asm.contig |2013-10-16 10:58:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.prokka/ray.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.ctg.fna |2013-10-16 10:58:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.prokka/ray.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.ctg.faa |2013-10-16 10:58:35| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.ctg.gene.cvg |2013-10-16 10:58:35| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.ctg.gene.map |2013-10-16 10:58:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna |2013-10-16 10:58:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna |2013-10-16 10:58:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna.bnk |2013-10-16 10:58:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna.bnk |2013-10-16 10:58:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa |2013-10-16 10:58:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa |2013-10-16 10:58:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa.bnk |2013-10-16 10:58:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa.bnk |2013-10-16 10:58:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.cvg |2013-10-16 10:58:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.cvg |2013-10-16 10:58:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.map |2013-10-16 10:58:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.gene.map |2013-10-16 10:58:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.faa |2013-10-16 10:58:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.fna |2013-10-16 10:58:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.75.asm.contig |2013-10-16 10:58:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 10:59:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.prokka --prefix ray.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.75.asm.contig |2013-10-16 10:59:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.prokka/ray.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.ctg.fna |2013-10-16 10:59:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.prokka/ray.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.ctg.faa |2013-10-16 10:59:19| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.ctg.gene.cvg |2013-10-16 10:59:19| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.ctg.gene.map |2013-10-16 10:59:19| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna |2013-10-16 10:59:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna |2013-10-16 10:59:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna.bnk |2013-10-16 10:59:20| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna.bnk |2013-10-16 10:59:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa |2013-10-16 10:59:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa |2013-10-16 10:59:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa.bnk |2013-10-16 10:59:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa.bnk |2013-10-16 10:59:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.cvg |2013-10-16 10:59:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.cvg |2013-10-16 10:59:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.map |2013-10-16 10:59:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.gene.map |2013-10-16 10:59:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.faa |2013-10-16 10:59:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.fna |2013-10-16 10:59:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.85.asm.contig |2013-10-16 10:59:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:00:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.prokka --prefix ray.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.85.asm.contig |2013-10-16 11:00:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.prokka/ray.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.ctg.fna |2013-10-16 11:00:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.prokka/ray.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.ctg.faa |2013-10-16 11:00:02| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.ctg.gene.cvg |2013-10-16 11:00:02| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.ctg.gene.map |2013-10-16 11:00:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna |2013-10-16 11:00:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna |2013-10-16 11:00:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna.bnk |2013-10-16 11:00:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna.bnk |2013-10-16 11:00:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa |2013-10-16 11:00:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa |2013-10-16 11:00:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa.bnk |2013-10-16 11:00:03| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa.bnk |2013-10-16 11:00:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.cvg |2013-10-16 11:00:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.cvg |2013-10-16 11:00:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.map |2013-10-16 11:00:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.gene.map |2013-10-16 11:00:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.faa |2013-10-16 11:00:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.fna |2013-10-16 11:00:03| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.95.asm.contig |2013-10-16 11:00:03| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:00:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.prokka --prefix ray.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ray.95.asm.contig |2013-10-16 11:00:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.prokka/ray.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.ctg.fna |2013-10-16 11:00:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.prokka/ray.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.ctg.faa |2013-10-16 11:00:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.ctg.gene.cvg |2013-10-16 11:00:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.ctg.gene.map |2013-10-16 11:00:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna |2013-10-16 11:00:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna |2013-10-16 11:00:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna.bnk |2013-10-16 11:00:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna.bnk |2013-10-16 11:00:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa |2013-10-16 11:00:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa |2013-10-16 11:00:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa.bnk |2013-10-16 11:00:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa.bnk |2013-10-16 11:00:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.cvg |2013-10-16 11:00:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.cvg |2013-10-16 11:00:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.map |2013-10-16 11:00:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.gene.map |2013-10-16 11:00:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.faa |2013-10-16 11:00:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/ray.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.fna |2013-10-16 11:00:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.105.asm.contig |2013-10-16 11:00:43| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:01:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.prokka --prefix sga.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.105.asm.contig |2013-10-16 11:01:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.prokka/sga.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.ctg.fna |2013-10-16 11:01:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.prokka/sga.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.ctg.faa |2013-10-16 11:01:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.ctg.gene.cvg |2013-10-16 11:01:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.ctg.gene.map |2013-10-16 11:01:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna |2013-10-16 11:01:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna |2013-10-16 11:01:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna.bnk |2013-10-16 11:01:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna.bnk |2013-10-16 11:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa |2013-10-16 11:01:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa |2013-10-16 11:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa.bnk |2013-10-16 11:01:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa.bnk |2013-10-16 11:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.cvg |2013-10-16 11:01:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.cvg |2013-10-16 11:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.map |2013-10-16 11:01:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.gene.map |2013-10-16 11:01:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.faa |2013-10-16 11:01:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.fna |2013-10-16 11:01:24| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.125.asm.contig |2013-10-16 11:01:24| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:02:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.prokka --prefix sga.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.125.asm.contig |2013-10-16 11:02:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.prokka/sga.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.ctg.fna |2013-10-16 11:02:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.prokka/sga.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.ctg.faa |2013-10-16 11:02:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.ctg.gene.cvg |2013-10-16 11:02:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.ctg.gene.map |2013-10-16 11:02:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna |2013-10-16 11:02:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna |2013-10-16 11:02:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna.bnk |2013-10-16 11:02:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna.bnk |2013-10-16 11:02:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa |2013-10-16 11:02:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa |2013-10-16 11:02:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa.bnk |2013-10-16 11:02:06| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa.bnk |2013-10-16 11:02:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.cvg |2013-10-16 11:02:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.cvg |2013-10-16 11:02:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.map |2013-10-16 11:02:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.gene.map |2013-10-16 11:02:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.faa |2013-10-16 11:02:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.fna |2013-10-16 11:02:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.25.asm.contig |2013-10-16 11:02:06| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:02:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.prokka --prefix sga.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.25.asm.contig |2013-10-16 11:02:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.prokka/sga.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.ctg.fna |2013-10-16 11:02:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.prokka/sga.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.ctg.faa |2013-10-16 11:02:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.ctg.gene.cvg |2013-10-16 11:02:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.ctg.gene.map |2013-10-16 11:02:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna |2013-10-16 11:02:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna |2013-10-16 11:02:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna.bnk |2013-10-16 11:02:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna.bnk |2013-10-16 11:02:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa |2013-10-16 11:02:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa |2013-10-16 11:02:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa.bnk |2013-10-16 11:02:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa.bnk |2013-10-16 11:02:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.cvg |2013-10-16 11:02:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.cvg |2013-10-16 11:02:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.map |2013-10-16 11:02:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.gene.map |2013-10-16 11:02:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.faa |2013-10-16 11:02:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.fna |2013-10-16 11:02:56| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.35.asm.contig |2013-10-16 11:02:56| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:03:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.prokka --prefix sga.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.35.asm.contig |2013-10-16 11:03:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.prokka/sga.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.ctg.fna |2013-10-16 11:03:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.prokka/sga.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.ctg.faa |2013-10-16 11:03:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.ctg.gene.cvg |2013-10-16 11:03:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.ctg.gene.map |2013-10-16 11:03:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna |2013-10-16 11:03:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna |2013-10-16 11:03:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna.bnk |2013-10-16 11:03:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna.bnk |2013-10-16 11:03:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa |2013-10-16 11:03:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa |2013-10-16 11:03:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa.bnk |2013-10-16 11:03:44| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa.bnk |2013-10-16 11:03:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.cvg |2013-10-16 11:03:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.cvg |2013-10-16 11:03:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.map |2013-10-16 11:03:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.gene.map |2013-10-16 11:03:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.faa |2013-10-16 11:03:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.fna |2013-10-16 11:03:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.41.asm.contig |2013-10-16 11:03:44| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:04:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.prokka --prefix sga.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.41.asm.contig |2013-10-16 11:04:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.prokka/sga.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.ctg.fna |2013-10-16 11:04:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.prokka/sga.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.ctg.faa |2013-10-16 11:04:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.ctg.gene.cvg |2013-10-16 11:04:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.ctg.gene.map |2013-10-16 11:04:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna |2013-10-16 11:04:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna |2013-10-16 11:04:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna.bnk |2013-10-16 11:04:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna.bnk |2013-10-16 11:04:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa |2013-10-16 11:04:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa |2013-10-16 11:04:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa.bnk |2013-10-16 11:04:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa.bnk |2013-10-16 11:04:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.cvg |2013-10-16 11:04:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.cvg |2013-10-16 11:04:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.map |2013-10-16 11:04:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.gene.map |2013-10-16 11:04:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.faa |2013-10-16 11:04:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.fna |2013-10-16 11:04:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.45.asm.contig |2013-10-16 11:04:29| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:05:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.prokka --prefix sga.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.45.asm.contig |2013-10-16 11:05:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.prokka/sga.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.ctg.fna |2013-10-16 11:05:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.prokka/sga.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.ctg.faa |2013-10-16 11:05:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.ctg.gene.cvg |2013-10-16 11:05:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.ctg.gene.map |2013-10-16 11:05:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna |2013-10-16 11:05:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna |2013-10-16 11:05:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna.bnk |2013-10-16 11:05:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna.bnk |2013-10-16 11:05:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa |2013-10-16 11:05:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa |2013-10-16 11:05:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa.bnk |2013-10-16 11:05:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa.bnk |2013-10-16 11:05:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.cvg |2013-10-16 11:05:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.cvg |2013-10-16 11:05:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.map |2013-10-16 11:05:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.gene.map |2013-10-16 11:05:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.faa |2013-10-16 11:05:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.fna |2013-10-16 11:05:15| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.55.asm.contig |2013-10-16 11:05:15| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:05:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.prokka --prefix sga.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.55.asm.contig |2013-10-16 11:05:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.prokka/sga.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.ctg.fna |2013-10-16 11:05:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.prokka/sga.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.ctg.faa |2013-10-16 11:05:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.ctg.gene.cvg |2013-10-16 11:05:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.ctg.gene.map |2013-10-16 11:05:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna |2013-10-16 11:05:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna |2013-10-16 11:05:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna.bnk |2013-10-16 11:05:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna.bnk |2013-10-16 11:05:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa |2013-10-16 11:05:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa |2013-10-16 11:05:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa.bnk |2013-10-16 11:05:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa.bnk |2013-10-16 11:05:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.cvg |2013-10-16 11:05:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.cvg |2013-10-16 11:05:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.map |2013-10-16 11:05:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.gene.map |2013-10-16 11:05:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.faa |2013-10-16 11:05:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.fna |2013-10-16 11:05:58| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.65.asm.contig |2013-10-16 11:05:58| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:06:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.prokka --prefix sga.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.65.asm.contig |2013-10-16 11:06:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.prokka/sga.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.ctg.fna |2013-10-16 11:06:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.prokka/sga.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.ctg.faa |2013-10-16 11:06:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.ctg.gene.cvg |2013-10-16 11:06:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.ctg.gene.map |2013-10-16 11:06:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna |2013-10-16 11:06:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna |2013-10-16 11:06:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna.bnk |2013-10-16 11:06:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna.bnk |2013-10-16 11:06:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa |2013-10-16 11:06:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa |2013-10-16 11:06:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa.bnk |2013-10-16 11:06:40| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa.bnk |2013-10-16 11:06:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.cvg |2013-10-16 11:06:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.cvg |2013-10-16 11:06:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.map |2013-10-16 11:06:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.gene.map |2013-10-16 11:06:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.faa |2013-10-16 11:06:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.fna |2013-10-16 11:06:40| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.75.asm.contig |2013-10-16 11:06:40| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:07:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.prokka --prefix sga.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.75.asm.contig |2013-10-16 11:07:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.prokka/sga.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.ctg.fna |2013-10-16 11:07:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.prokka/sga.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.ctg.faa |2013-10-16 11:07:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.ctg.gene.cvg |2013-10-16 11:07:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.ctg.gene.map |2013-10-16 11:07:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna |2013-10-16 11:07:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna |2013-10-16 11:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna.bnk |2013-10-16 11:07:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna.bnk |2013-10-16 11:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa |2013-10-16 11:07:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa |2013-10-16 11:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa.bnk |2013-10-16 11:07:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa.bnk |2013-10-16 11:07:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.cvg |2013-10-16 11:07:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.cvg |2013-10-16 11:07:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.map |2013-10-16 11:07:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.gene.map |2013-10-16 11:07:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.faa |2013-10-16 11:07:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.fna |2013-10-16 11:07:22| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.85.asm.contig |2013-10-16 11:07:22| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:08:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.prokka --prefix sga.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.85.asm.contig |2013-10-16 11:08:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.prokka/sga.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.ctg.fna |2013-10-16 11:08:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.prokka/sga.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.ctg.faa |2013-10-16 11:08:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.ctg.gene.cvg |2013-10-16 11:08:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.ctg.gene.map |2013-10-16 11:08:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna |2013-10-16 11:08:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna |2013-10-16 11:08:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna.bnk |2013-10-16 11:08:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna.bnk |2013-10-16 11:08:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa |2013-10-16 11:08:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa |2013-10-16 11:08:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa.bnk |2013-10-16 11:08:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa.bnk |2013-10-16 11:08:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.cvg |2013-10-16 11:08:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.cvg |2013-10-16 11:08:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.map |2013-10-16 11:08:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.gene.map |2013-10-16 11:08:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.faa |2013-10-16 11:08:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.fna |2013-10-16 11:08:02| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.95.asm.contig |2013-10-16 11:08:02| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:08:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.prokka --prefix sga.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sga.95.asm.contig |2013-10-16 11:08:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.prokka/sga.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.ctg.fna |2013-10-16 11:08:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.prokka/sga.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.ctg.faa |2013-10-16 11:08:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.ctg.gene.cvg |2013-10-16 11:08:46| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.ctg.gene.map |2013-10-16 11:08:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna |2013-10-16 11:08:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna |2013-10-16 11:08:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna.bnk |2013-10-16 11:08:47| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna.bnk |2013-10-16 11:08:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa |2013-10-16 11:08:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa |2013-10-16 11:08:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa.bnk |2013-10-16 11:08:47| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa.bnk |2013-10-16 11:08:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.cvg |2013-10-16 11:08:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.cvg |2013-10-16 11:08:47| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.map |2013-10-16 11:08:47| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.gene.map |2013-10-16 11:08:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.faa |2013-10-16 11:08:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sga.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.fna |2013-10-16 11:08:48| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.25.asm.contig |2013-10-16 11:08:48| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 11:37:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.prokka --prefix soapdenovo2.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.25.asm.contig |2013-10-16 12:06:28|# [FINDORFS] |2013-10-16 12:06:28| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.25.asm.contig |2013-10-16 12:06:28| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:32:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.prokka --prefix soapdenovo2.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.25.asm.contig |2013-10-16 12:32:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.prokka/soapdenovo2.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.ctg.fna |2013-10-16 12:32:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.prokka/soapdenovo2.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.ctg.faa |2013-10-16 12:32:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.ctg.gene.cvg |2013-10-16 12:32:36| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.ctg.gene.map |2013-10-16 12:32:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna |2013-10-16 12:32:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna |2013-10-16 12:32:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna.bnk |2013-10-16 12:32:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna.bnk |2013-10-16 12:32:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa |2013-10-16 12:32:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa |2013-10-16 12:32:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa.bnk |2013-10-16 12:32:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa.bnk |2013-10-16 12:32:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.cvg |2013-10-16 12:32:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.cvg |2013-10-16 12:32:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.map |2013-10-16 12:32:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.gene.map |2013-10-16 12:32:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.faa |2013-10-16 12:32:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.fna |2013-10-16 12:32:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.35.asm.contig |2013-10-16 12:32:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:33:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.prokka --prefix soapdenovo2.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.35.asm.contig |2013-10-16 12:33:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.prokka/soapdenovo2.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.ctg.fna |2013-10-16 12:33:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.prokka/soapdenovo2.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.ctg.faa |2013-10-16 12:33:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.ctg.gene.cvg |2013-10-16 12:33:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.ctg.gene.map |2013-10-16 12:33:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna |2013-10-16 12:33:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna |2013-10-16 12:33:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna.bnk |2013-10-16 12:33:20| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna.bnk |2013-10-16 12:33:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa |2013-10-16 12:33:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa |2013-10-16 12:33:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa.bnk |2013-10-16 12:33:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa.bnk |2013-10-16 12:33:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.cvg |2013-10-16 12:33:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.cvg |2013-10-16 12:33:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.map |2013-10-16 12:33:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.gene.map |2013-10-16 12:33:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.faa |2013-10-16 12:33:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.fna |2013-10-16 12:33:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.41.asm.contig |2013-10-16 12:33:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:34:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.prokka --prefix soapdenovo2.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.41.asm.contig |2013-10-16 12:34:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.prokka/soapdenovo2.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.ctg.fna |2013-10-16 12:34:03| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.prokka/soapdenovo2.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.ctg.faa |2013-10-16 12:34:03| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.ctg.gene.cvg |2013-10-16 12:34:03| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.ctg.gene.map |2013-10-16 12:34:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna |2013-10-16 12:34:03| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna |2013-10-16 12:34:03| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna.bnk |2013-10-16 12:34:04| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna.bnk |2013-10-16 12:34:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa |2013-10-16 12:34:04| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa |2013-10-16 12:34:04| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa.bnk |2013-10-16 12:34:05| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa.bnk |2013-10-16 12:34:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.cvg |2013-10-16 12:34:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.cvg |2013-10-16 12:34:05| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.map |2013-10-16 12:34:05| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.gene.map |2013-10-16 12:34:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.faa |2013-10-16 12:34:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.fna |2013-10-16 12:34:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.45.asm.contig |2013-10-16 12:34:06| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:34:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.prokka --prefix soapdenovo2.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.45.asm.contig |2013-10-16 12:34:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.prokka/soapdenovo2.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.ctg.fna |2013-10-16 12:34:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.prokka/soapdenovo2.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.ctg.faa |2013-10-16 12:34:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.ctg.gene.cvg |2013-10-16 12:34:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.ctg.gene.map |2013-10-16 12:34:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna |2013-10-16 12:34:48| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna |2013-10-16 12:34:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna.bnk |2013-10-16 12:34:49| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna.bnk |2013-10-16 12:34:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa |2013-10-16 12:34:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa |2013-10-16 12:34:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa.bnk |2013-10-16 12:34:49| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa.bnk |2013-10-16 12:34:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.cvg |2013-10-16 12:34:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.cvg |2013-10-16 12:34:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.map |2013-10-16 12:34:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.gene.map |2013-10-16 12:34:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.faa |2013-10-16 12:34:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.fna |2013-10-16 12:34:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.55.asm.contig |2013-10-16 12:34:50| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:35:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.prokka --prefix soapdenovo2.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.55.asm.contig |2013-10-16 12:35:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.prokka/soapdenovo2.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.ctg.fna |2013-10-16 12:35:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.prokka/soapdenovo2.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.ctg.faa |2013-10-16 12:35:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.ctg.gene.cvg |2013-10-16 12:35:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.ctg.gene.map |2013-10-16 12:35:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna |2013-10-16 12:35:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna |2013-10-16 12:35:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna.bnk |2013-10-16 12:35:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna.bnk |2013-10-16 12:35:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa |2013-10-16 12:35:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa |2013-10-16 12:35:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa.bnk |2013-10-16 12:35:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa.bnk |2013-10-16 12:35:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.cvg |2013-10-16 12:35:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.cvg |2013-10-16 12:35:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.map |2013-10-16 12:35:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.gene.map |2013-10-16 12:35:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.faa |2013-10-16 12:35:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.fna |2013-10-16 12:35:34| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.65.asm.contig |2013-10-16 12:35:34| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:36:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.prokka --prefix soapdenovo2.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.65.asm.contig |2013-10-16 12:36:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.prokka/soapdenovo2.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.ctg.fna |2013-10-16 12:36:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.prokka/soapdenovo2.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.ctg.faa |2013-10-16 12:36:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.ctg.gene.cvg |2013-10-16 12:36:15| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.ctg.gene.map |2013-10-16 12:36:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna |2013-10-16 12:36:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna |2013-10-16 12:36:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna.bnk |2013-10-16 12:36:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna.bnk |2013-10-16 12:36:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa |2013-10-16 12:36:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa |2013-10-16 12:36:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa.bnk |2013-10-16 12:36:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa.bnk |2013-10-16 12:36:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.cvg |2013-10-16 12:36:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.cvg |2013-10-16 12:36:16| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.map |2013-10-16 12:36:16| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.gene.map |2013-10-16 12:36:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.faa |2013-10-16 12:36:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.fna |2013-10-16 12:36:16| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.75.asm.contig |2013-10-16 12:36:16| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:36:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.prokka --prefix soapdenovo2.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.75.asm.contig |2013-10-16 12:36:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.prokka/soapdenovo2.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.ctg.fna |2013-10-16 12:36:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.prokka/soapdenovo2.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.ctg.faa |2013-10-16 12:36:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.ctg.gene.cvg |2013-10-16 12:36:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.ctg.gene.map |2013-10-16 12:36:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna |2013-10-16 12:36:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna |2013-10-16 12:36:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna.bnk |2013-10-16 12:36:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna.bnk |2013-10-16 12:36:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa |2013-10-16 12:36:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa |2013-10-16 12:36:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa.bnk |2013-10-16 12:36:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa.bnk |2013-10-16 12:36:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.cvg |2013-10-16 12:36:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.cvg |2013-10-16 12:36:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.map |2013-10-16 12:36:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.gene.map |2013-10-16 12:36:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.faa |2013-10-16 12:36:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.fna |2013-10-16 12:36:58| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.85.asm.contig |2013-10-16 12:36:58| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.prokka --prefix soapdenovo2.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.85.asm.contig |2013-10-16 12:37:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.prokka/soapdenovo2.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.ctg.fna |2013-10-16 12:37:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.prokka/soapdenovo2.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.ctg.faa |2013-10-16 12:37:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.ctg.gene.cvg |2013-10-16 12:37:33| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.ctg.gene.map |2013-10-16 12:37:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna |2013-10-16 12:37:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna |2013-10-16 12:37:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna.bnk |2013-10-16 12:37:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna.bnk |2013-10-16 12:37:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa |2013-10-16 12:37:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa |2013-10-16 12:37:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa.bnk |2013-10-16 12:37:34| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa.bnk |2013-10-16 12:37:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.cvg |2013-10-16 12:37:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.cvg |2013-10-16 12:37:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.map |2013-10-16 12:37:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.gene.map |2013-10-16 12:37:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.faa |2013-10-16 12:37:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.fna |2013-10-16 12:37:34| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.95.asm.contig |2013-10-16 12:37:34| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:37:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.prokka --prefix soapdenovo2.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/soapdenovo2.95.asm.contig |2013-10-16 12:37:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.prokka/soapdenovo2.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.ctg.fna |2013-10-16 12:37:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.prokka/soapdenovo2.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.ctg.faa |2013-10-16 12:37:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.ctg.gene.cvg |2013-10-16 12:37:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.ctg.gene.map |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna |2013-10-16 12:37:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna.bnk |2013-10-16 12:37:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna.bnk |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa |2013-10-16 12:37:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa.bnk |2013-10-16 12:37:37| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa.bnk |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.cvg |2013-10-16 12:37:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.cvg |2013-10-16 12:37:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.map |2013-10-16 12:37:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.gene.map |2013-10-16 12:37:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.faa |2013-10-16 12:37:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/soapdenovo2.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.fna |2013-10-16 12:37:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.105.asm.contig |2013-10-16 12:37:37| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:38:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.prokka --prefix spades.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.105.asm.contig |2013-10-16 12:38:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.prokka/spades.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.ctg.fna |2013-10-16 12:38:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.prokka/spades.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.ctg.faa |2013-10-16 12:38:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.ctg.gene.cvg |2013-10-16 12:38:21| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.ctg.gene.map |2013-10-16 12:38:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna |2013-10-16 12:38:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna |2013-10-16 12:38:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna.bnk |2013-10-16 12:38:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna.bnk |2013-10-16 12:38:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa |2013-10-16 12:38:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa |2013-10-16 12:38:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa.bnk |2013-10-16 12:38:22| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa.bnk |2013-10-16 12:38:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.cvg |2013-10-16 12:38:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.cvg |2013-10-16 12:38:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.map |2013-10-16 12:38:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.gene.map |2013-10-16 12:38:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.faa |2013-10-16 12:38:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.fna |2013-10-16 12:38:22| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.125.asm.contig |2013-10-16 12:38:22| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:39:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.prokka --prefix spades.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.125.asm.contig |2013-10-16 12:39:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.prokka/spades.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.ctg.fna |2013-10-16 12:39:06| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.prokka/spades.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.ctg.faa |2013-10-16 12:39:06| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.ctg.gene.cvg |2013-10-16 12:39:06| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.ctg.gene.map |2013-10-16 12:39:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna |2013-10-16 12:39:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna |2013-10-16 12:39:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna.bnk |2013-10-16 12:39:07| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna.bnk |2013-10-16 12:39:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa |2013-10-16 12:39:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa |2013-10-16 12:39:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa.bnk |2013-10-16 12:39:07| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa.bnk |2013-10-16 12:39:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.cvg |2013-10-16 12:39:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.cvg |2013-10-16 12:39:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.map |2013-10-16 12:39:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.gene.map |2013-10-16 12:39:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.faa |2013-10-16 12:39:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.fna |2013-10-16 12:39:08| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.25.asm.contig |2013-10-16 12:39:08| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:39:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.prokka --prefix spades.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.25.asm.contig |2013-10-16 12:39:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.prokka/spades.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.ctg.fna |2013-10-16 12:39:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.prokka/spades.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.ctg.faa |2013-10-16 12:39:52| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.ctg.gene.cvg |2013-10-16 12:39:52| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.ctg.gene.map |2013-10-16 12:39:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna |2013-10-16 12:39:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna |2013-10-16 12:39:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna.bnk |2013-10-16 12:39:52| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna.bnk |2013-10-16 12:39:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa |2013-10-16 12:39:52| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa |2013-10-16 12:39:52| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa.bnk |2013-10-16 12:39:53| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa.bnk |2013-10-16 12:39:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.cvg |2013-10-16 12:39:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.cvg |2013-10-16 12:39:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.map |2013-10-16 12:39:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.gene.map |2013-10-16 12:39:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.faa |2013-10-16 12:39:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.fna |2013-10-16 12:39:53| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.35.asm.contig |2013-10-16 12:39:53| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:40:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.prokka --prefix spades.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.35.asm.contig |2013-10-16 12:40:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.prokka/spades.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.ctg.fna |2013-10-16 12:40:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.prokka/spades.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.ctg.faa |2013-10-16 12:40:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.ctg.gene.cvg |2013-10-16 12:40:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.ctg.gene.map |2013-10-16 12:40:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna |2013-10-16 12:40:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna |2013-10-16 12:40:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna.bnk |2013-10-16 12:40:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna.bnk |2013-10-16 12:40:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa |2013-10-16 12:40:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa |2013-10-16 12:40:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa.bnk |2013-10-16 12:40:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa.bnk |2013-10-16 12:40:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.cvg |2013-10-16 12:40:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.cvg |2013-10-16 12:40:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.map |2013-10-16 12:40:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.gene.map |2013-10-16 12:40:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.faa |2013-10-16 12:40:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.fna |2013-10-16 12:40:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.41.asm.contig |2013-10-16 12:40:39| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:41:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.prokka --prefix spades.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.41.asm.contig |2013-10-16 12:41:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.prokka/spades.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.ctg.fna |2013-10-16 12:41:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.prokka/spades.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.ctg.faa |2013-10-16 12:41:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.ctg.gene.cvg |2013-10-16 12:41:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.ctg.gene.map |2013-10-16 12:41:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna |2013-10-16 12:41:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna |2013-10-16 12:41:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna.bnk |2013-10-16 12:41:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna.bnk |2013-10-16 12:41:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa |2013-10-16 12:41:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa |2013-10-16 12:41:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa.bnk |2013-10-16 12:41:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa.bnk |2013-10-16 12:41:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.cvg |2013-10-16 12:41:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.cvg |2013-10-16 12:41:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.map |2013-10-16 12:41:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.gene.map |2013-10-16 12:41:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.faa |2013-10-16 12:41:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.fna |2013-10-16 12:41:24| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.45.asm.contig |2013-10-16 12:41:24| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:42:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.prokka --prefix spades.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.45.asm.contig |2013-10-16 12:42:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.prokka/spades.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.ctg.fna |2013-10-16 12:42:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.prokka/spades.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.ctg.faa |2013-10-16 12:42:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.ctg.gene.cvg |2013-10-16 12:42:08| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.ctg.gene.map |2013-10-16 12:42:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna |2013-10-16 12:42:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna |2013-10-16 12:42:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna.bnk |2013-10-16 12:42:09| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna.bnk |2013-10-16 12:42:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa |2013-10-16 12:42:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa |2013-10-16 12:42:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa.bnk |2013-10-16 12:42:09| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa.bnk |2013-10-16 12:42:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.cvg |2013-10-16 12:42:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.cvg |2013-10-16 12:42:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.map |2013-10-16 12:42:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.gene.map |2013-10-16 12:42:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.faa |2013-10-16 12:42:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.fna |2013-10-16 12:42:09| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.55.asm.contig |2013-10-16 12:42:10| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:42:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.prokka --prefix spades.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.55.asm.contig |2013-10-16 12:42:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.prokka/spades.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.ctg.fna |2013-10-16 12:42:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.prokka/spades.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.ctg.faa |2013-10-16 12:42:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.ctg.gene.cvg |2013-10-16 12:42:53| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.ctg.gene.map |2013-10-16 12:42:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna |2013-10-16 12:42:53| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna |2013-10-16 12:42:53| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna.bnk |2013-10-16 12:42:54| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna.bnk |2013-10-16 12:42:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa |2013-10-16 12:42:54| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa |2013-10-16 12:42:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa.bnk |2013-10-16 12:42:54| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa.bnk |2013-10-16 12:42:54| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.cvg |2013-10-16 12:42:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.cvg |2013-10-16 12:42:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.map |2013-10-16 12:42:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.gene.map |2013-10-16 12:42:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.faa |2013-10-16 12:42:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.fna |2013-10-16 12:42:55| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.65.asm.contig |2013-10-16 12:42:55| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:43:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.prokka --prefix spades.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.65.asm.contig |2013-10-16 12:43:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.prokka/spades.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.ctg.fna |2013-10-16 12:43:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.prokka/spades.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.ctg.faa |2013-10-16 12:43:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.ctg.gene.cvg |2013-10-16 12:43:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.ctg.gene.map |2013-10-16 12:43:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna |2013-10-16 12:43:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna |2013-10-16 12:43:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna.bnk |2013-10-16 12:43:39| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna.bnk |2013-10-16 12:43:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa |2013-10-16 12:43:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa |2013-10-16 12:43:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa.bnk |2013-10-16 12:43:40| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa.bnk |2013-10-16 12:43:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.cvg |2013-10-16 12:43:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.cvg |2013-10-16 12:43:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.map |2013-10-16 12:43:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.gene.map |2013-10-16 12:43:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.faa |2013-10-16 12:43:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.fna |2013-10-16 12:43:40| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.75.asm.contig |2013-10-16 12:43:40| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:44:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.prokka --prefix spades.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.75.asm.contig |2013-10-16 12:44:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.prokka/spades.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.ctg.fna |2013-10-16 12:44:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.prokka/spades.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.ctg.faa |2013-10-16 12:44:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.ctg.gene.cvg |2013-10-16 12:44:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.ctg.gene.map |2013-10-16 12:44:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna |2013-10-16 12:44:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna |2013-10-16 12:44:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna.bnk |2013-10-16 12:44:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna.bnk |2013-10-16 12:44:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa |2013-10-16 12:44:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa |2013-10-16 12:44:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa.bnk |2013-10-16 12:44:25| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa.bnk |2013-10-16 12:44:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.cvg |2013-10-16 12:44:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.cvg |2013-10-16 12:44:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.map |2013-10-16 12:44:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.gene.map |2013-10-16 12:44:25| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.faa |2013-10-16 12:44:25| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.fna |2013-10-16 12:44:25| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.85.asm.contig |2013-10-16 12:44:25| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:45:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.prokka --prefix spades.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.85.asm.contig |2013-10-16 12:45:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.prokka/spades.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.ctg.fna |2013-10-16 12:45:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.prokka/spades.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.ctg.faa |2013-10-16 12:45:09| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.ctg.gene.cvg |2013-10-16 12:45:09| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.ctg.gene.map |2013-10-16 12:45:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna |2013-10-16 12:45:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna |2013-10-16 12:45:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna.bnk |2013-10-16 12:45:10| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna.bnk |2013-10-16 12:45:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa |2013-10-16 12:45:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa |2013-10-16 12:45:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa.bnk |2013-10-16 12:45:10| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa.bnk |2013-10-16 12:45:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.cvg |2013-10-16 12:45:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.cvg |2013-10-16 12:45:11| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.map |2013-10-16 12:45:11| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.gene.map |2013-10-16 12:45:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.faa |2013-10-16 12:45:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.fna |2013-10-16 12:45:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.95.asm.contig |2013-10-16 12:45:11| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:45:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.prokka --prefix spades.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/spades.95.asm.contig |2013-10-16 12:45:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.prokka/spades.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.ctg.fna |2013-10-16 12:45:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.prokka/spades.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.ctg.faa |2013-10-16 12:45:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.ctg.gene.cvg |2013-10-16 12:45:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.ctg.gene.map |2013-10-16 12:45:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna |2013-10-16 12:45:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna |2013-10-16 12:45:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna.bnk |2013-10-16 12:45:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna.bnk |2013-10-16 12:45:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa |2013-10-16 12:45:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa |2013-10-16 12:45:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa.bnk |2013-10-16 12:45:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa.bnk |2013-10-16 12:45:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.cvg |2013-10-16 12:45:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.cvg |2013-10-16 12:45:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.map |2013-10-16 12:45:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.gene.map |2013-10-16 12:45:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.faa |2013-10-16 12:45:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/spades.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.fna |2013-10-16 12:45:56| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.105.asm.contig |2013-10-16 12:45:56| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:46:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.prokka --prefix sparseassembler.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.105.asm.contig |2013-10-16 12:46:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.prokka/sparseassembler.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.ctg.fna |2013-10-16 12:46:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.prokka/sparseassembler.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.ctg.faa |2013-10-16 12:46:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.ctg.gene.cvg |2013-10-16 12:46:57| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.ctg.gene.map |2013-10-16 12:46:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna |2013-10-16 12:46:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna |2013-10-16 12:46:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna.bnk |2013-10-16 12:46:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna.bnk |2013-10-16 12:46:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa |2013-10-16 12:46:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa |2013-10-16 12:46:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa.bnk |2013-10-16 12:46:58| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa.bnk |2013-10-16 12:46:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.cvg |2013-10-16 12:46:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.cvg |2013-10-16 12:46:58| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.map |2013-10-16 12:46:58| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.gene.map |2013-10-16 12:46:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.faa |2013-10-16 12:46:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.fna |2013-10-16 12:46:58| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.125.asm.contig |2013-10-16 12:46:58| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:48:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.prokka --prefix sparseassembler.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.125.asm.contig |2013-10-16 12:48:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.prokka/sparseassembler.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.ctg.fna |2013-10-16 12:48:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.prokka/sparseassembler.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.ctg.faa |2013-10-16 12:48:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.ctg.gene.cvg |2013-10-16 12:48:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.ctg.gene.map |2013-10-16 12:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna |2013-10-16 12:48:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna |2013-10-16 12:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna.bnk |2013-10-16 12:48:20| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna.bnk |2013-10-16 12:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa |2013-10-16 12:48:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa |2013-10-16 12:48:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa.bnk |2013-10-16 12:48:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa.bnk |2013-10-16 12:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.cvg |2013-10-16 12:48:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.cvg |2013-10-16 12:48:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.map |2013-10-16 12:48:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.gene.map |2013-10-16 12:48:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.faa |2013-10-16 12:48:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.fna |2013-10-16 12:48:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.25.asm.contig |2013-10-16 12:48:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:49:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.prokka --prefix sparseassembler.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.25.asm.contig |2013-10-16 12:49:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.prokka/sparseassembler.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.ctg.fna |2013-10-16 12:49:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.prokka/sparseassembler.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.ctg.faa |2013-10-16 12:49:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.ctg.gene.cvg |2013-10-16 12:49:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.ctg.gene.map |2013-10-16 12:49:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna |2013-10-16 12:49:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna |2013-10-16 12:49:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna.bnk |2013-10-16 12:49:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna.bnk |2013-10-16 12:49:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa |2013-10-16 12:49:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa |2013-10-16 12:49:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa.bnk |2013-10-16 12:49:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa.bnk |2013-10-16 12:49:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.cvg |2013-10-16 12:49:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.cvg |2013-10-16 12:49:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.map |2013-10-16 12:49:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.gene.map |2013-10-16 12:49:30| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.faa |2013-10-16 12:49:30| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.fna |2013-10-16 12:49:30| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.35.asm.contig |2013-10-16 12:49:30| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:50:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.prokka --prefix sparseassembler.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.35.asm.contig |2013-10-16 12:50:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.prokka/sparseassembler.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.ctg.fna |2013-10-16 12:50:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.prokka/sparseassembler.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.ctg.faa |2013-10-16 12:50:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.ctg.gene.cvg |2013-10-16 12:50:28| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.ctg.gene.map |2013-10-16 12:50:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna |2013-10-16 12:50:28| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna |2013-10-16 12:50:28| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna.bnk |2013-10-16 12:50:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna.bnk |2013-10-16 12:50:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa |2013-10-16 12:50:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa |2013-10-16 12:50:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa.bnk |2013-10-16 12:50:29| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa.bnk |2013-10-16 12:50:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.cvg |2013-10-16 12:50:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.cvg |2013-10-16 12:50:29| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.map |2013-10-16 12:50:29| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.gene.map |2013-10-16 12:50:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.faa |2013-10-16 12:50:29| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.fna |2013-10-16 12:50:29| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.41.asm.contig |2013-10-16 12:50:29| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:51:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.prokka --prefix sparseassembler.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.41.asm.contig |2013-10-16 12:51:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.prokka/sparseassembler.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.ctg.fna |2013-10-16 12:51:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.prokka/sparseassembler.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.ctg.faa |2013-10-16 12:51:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.ctg.gene.cvg |2013-10-16 12:51:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.ctg.gene.map |2013-10-16 12:51:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna |2013-10-16 12:51:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna |2013-10-16 12:51:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna.bnk |2013-10-16 12:51:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna.bnk |2013-10-16 12:51:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa |2013-10-16 12:51:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa |2013-10-16 12:51:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa.bnk |2013-10-16 12:51:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa.bnk |2013-10-16 12:51:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.cvg |2013-10-16 12:51:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.cvg |2013-10-16 12:51:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.map |2013-10-16 12:51:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.gene.map |2013-10-16 12:51:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.faa |2013-10-16 12:51:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.fna |2013-10-16 12:51:24| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.45.asm.contig |2013-10-16 12:51:24| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:52:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.prokka --prefix sparseassembler.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.45.asm.contig |2013-10-16 12:52:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.prokka/sparseassembler.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.ctg.fna |2013-10-16 12:52:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.prokka/sparseassembler.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.ctg.faa |2013-10-16 12:52:14| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.ctg.gene.cvg |2013-10-16 12:52:14| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.ctg.gene.map |2013-10-16 12:52:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna |2013-10-16 12:52:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna |2013-10-16 12:52:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna.bnk |2013-10-16 12:52:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna.bnk |2013-10-16 12:52:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa |2013-10-16 12:52:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa |2013-10-16 12:52:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa.bnk |2013-10-16 12:52:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa.bnk |2013-10-16 12:52:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.cvg |2013-10-16 12:52:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.cvg |2013-10-16 12:52:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.map |2013-10-16 12:52:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.gene.map |2013-10-16 12:52:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.faa |2013-10-16 12:52:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.fna |2013-10-16 12:52:15| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.55.asm.contig |2013-10-16 12:52:15| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:53:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.prokka --prefix sparseassembler.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.55.asm.contig |2013-10-16 12:53:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.prokka/sparseassembler.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.ctg.fna |2013-10-16 12:53:05| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.prokka/sparseassembler.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.ctg.faa |2013-10-16 12:53:05| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.ctg.gene.cvg |2013-10-16 12:53:06| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.ctg.gene.map |2013-10-16 12:53:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna |2013-10-16 12:53:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna |2013-10-16 12:53:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna.bnk |2013-10-16 12:53:06| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna.bnk |2013-10-16 12:53:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa |2013-10-16 12:53:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa |2013-10-16 12:53:06| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa.bnk |2013-10-16 12:53:07| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa.bnk |2013-10-16 12:53:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.cvg |2013-10-16 12:53:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.cvg |2013-10-16 12:53:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.map |2013-10-16 12:53:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.gene.map |2013-10-16 12:53:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.faa |2013-10-16 12:53:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.fna |2013-10-16 12:53:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.65.asm.contig |2013-10-16 12:53:07| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:53:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.prokka --prefix sparseassembler.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.65.asm.contig |2013-10-16 12:53:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.prokka/sparseassembler.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.ctg.fna |2013-10-16 12:53:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.prokka/sparseassembler.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.ctg.faa |2013-10-16 12:53:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.ctg.gene.cvg |2013-10-16 12:53:59| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.ctg.gene.map |2013-10-16 12:53:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna |2013-10-16 12:53:59| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna |2013-10-16 12:53:59| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna.bnk |2013-10-16 12:54:00| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna.bnk |2013-10-16 12:54:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa |2013-10-16 12:54:00| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa |2013-10-16 12:54:00| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa.bnk |2013-10-16 12:54:01| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa.bnk |2013-10-16 12:54:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.cvg |2013-10-16 12:54:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.cvg |2013-10-16 12:54:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.map |2013-10-16 12:54:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.gene.map |2013-10-16 12:54:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.faa |2013-10-16 12:54:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.fna |2013-10-16 12:54:01| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.75.asm.contig |2013-10-16 12:54:01| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:54:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.prokka --prefix sparseassembler.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.75.asm.contig |2013-10-16 12:54:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.prokka/sparseassembler.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.ctg.fna |2013-10-16 12:54:55| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.prokka/sparseassembler.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.ctg.faa |2013-10-16 12:54:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.ctg.gene.cvg |2013-10-16 12:54:55| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.ctg.gene.map |2013-10-16 12:54:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna |2013-10-16 12:54:55| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna |2013-10-16 12:54:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna.bnk |2013-10-16 12:54:55| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna.bnk |2013-10-16 12:54:55| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa |2013-10-16 12:54:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa |2013-10-16 12:54:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa.bnk |2013-10-16 12:54:56| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa.bnk |2013-10-16 12:54:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.cvg |2013-10-16 12:54:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.cvg |2013-10-16 12:54:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.map |2013-10-16 12:54:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.gene.map |2013-10-16 12:54:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.faa |2013-10-16 12:54:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.fna |2013-10-16 12:54:56| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.85.asm.contig |2013-10-16 12:54:56| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:55:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.prokka --prefix sparseassembler.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.85.asm.contig |2013-10-16 12:55:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.prokka/sparseassembler.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.ctg.fna |2013-10-16 12:55:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.prokka/sparseassembler.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.ctg.faa |2013-10-16 12:55:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.ctg.gene.cvg |2013-10-16 12:55:48| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.ctg.gene.map |2013-10-16 12:55:48| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna |2013-10-16 12:55:48| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna |2013-10-16 12:55:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna.bnk |2013-10-16 12:55:49| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna.bnk |2013-10-16 12:55:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa |2013-10-16 12:55:49| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa |2013-10-16 12:55:49| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa.bnk |2013-10-16 12:55:50| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa.bnk |2013-10-16 12:55:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.cvg |2013-10-16 12:55:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.cvg |2013-10-16 12:55:50| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.map |2013-10-16 12:55:50| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.gene.map |2013-10-16 12:55:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.faa |2013-10-16 12:55:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.fna |2013-10-16 12:55:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.95.asm.contig |2013-10-16 12:55:50| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:56:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.prokka --prefix sparseassembler.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/sparseassembler.95.asm.contig |2013-10-16 12:56:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.prokka/sparseassembler.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.ctg.fna |2013-10-16 12:56:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.prokka/sparseassembler.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.ctg.faa |2013-10-16 12:56:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.ctg.gene.cvg |2013-10-16 12:56:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.ctg.gene.map |2013-10-16 12:56:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna |2013-10-16 12:56:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna |2013-10-16 12:56:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna.bnk |2013-10-16 12:56:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna.bnk |2013-10-16 12:56:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa |2013-10-16 12:56:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa |2013-10-16 12:56:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa.bnk |2013-10-16 12:56:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa.bnk |2013-10-16 12:56:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.cvg |2013-10-16 12:56:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.cvg |2013-10-16 12:56:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.map |2013-10-16 12:56:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.gene.map |2013-10-16 12:56:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.faa |2013-10-16 12:56:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/sparseassembler.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.fna |2013-10-16 12:56:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.105.asm.contig |2013-10-16 12:56:47| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:57:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.prokka --prefix velvet-sc.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.105.asm.contig |2013-10-16 12:57:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.prokka/velvet-sc.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.ctg.fna |2013-10-16 12:57:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.prokka/velvet-sc.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.ctg.faa |2013-10-16 12:57:31| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.ctg.gene.cvg |2013-10-16 12:57:31| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.ctg.gene.map |2013-10-16 12:57:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna |2013-10-16 12:57:31| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna |2013-10-16 12:57:31| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna.bnk |2013-10-16 12:57:32| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna.bnk |2013-10-16 12:57:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa |2013-10-16 12:57:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa |2013-10-16 12:57:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa.bnk |2013-10-16 12:57:32| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa.bnk |2013-10-16 12:57:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.cvg |2013-10-16 12:57:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.cvg |2013-10-16 12:57:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.map |2013-10-16 12:57:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.gene.map |2013-10-16 12:57:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.faa |2013-10-16 12:57:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.fna |2013-10-16 12:57:33| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.125.asm.contig |2013-10-16 12:57:33| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:58:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.prokka --prefix velvet-sc.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.125.asm.contig |2013-10-16 12:58:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.prokka/velvet-sc.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.ctg.fna |2013-10-16 12:58:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.prokka/velvet-sc.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.ctg.faa |2013-10-16 12:58:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.ctg.gene.cvg |2013-10-16 12:58:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.ctg.gene.map |2013-10-16 12:58:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna |2013-10-16 12:58:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna |2013-10-16 12:58:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna.bnk |2013-10-16 12:58:32| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna.bnk |2013-10-16 12:58:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa |2013-10-16 12:58:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa |2013-10-16 12:58:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa.bnk |2013-10-16 12:58:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa.bnk |2013-10-16 12:58:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.cvg |2013-10-16 12:58:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.cvg |2013-10-16 12:58:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.map |2013-10-16 12:58:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.gene.map |2013-10-16 12:58:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.faa |2013-10-16 12:58:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.fna |2013-10-16 12:58:33| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.25.asm.contig |2013-10-16 12:58:33| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:59:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.prokka --prefix velvet-sc.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.25.asm.contig |2013-10-16 12:59:12| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.prokka/velvet-sc.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.ctg.fna |2013-10-16 12:59:12| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.prokka/velvet-sc.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.ctg.faa |2013-10-16 12:59:12| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.ctg.gene.cvg |2013-10-16 12:59:12| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.ctg.gene.map |2013-10-16 12:59:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna |2013-10-16 12:59:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna |2013-10-16 12:59:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna.bnk |2013-10-16 12:59:13| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna.bnk |2013-10-16 12:59:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa |2013-10-16 12:59:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa |2013-10-16 12:59:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa.bnk |2013-10-16 12:59:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa.bnk |2013-10-16 12:59:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.cvg |2013-10-16 12:59:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.cvg |2013-10-16 12:59:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.map |2013-10-16 12:59:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.gene.map |2013-10-16 12:59:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.faa |2013-10-16 12:59:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.fna |2013-10-16 12:59:14| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.35.asm.contig |2013-10-16 12:59:14| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 12:59:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.prokka --prefix velvet-sc.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.35.asm.contig |2013-10-16 12:59:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.prokka/velvet-sc.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.ctg.fna |2013-10-16 12:59:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.prokka/velvet-sc.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.ctg.faa |2013-10-16 12:59:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.ctg.gene.cvg |2013-10-16 12:59:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.ctg.gene.map |2013-10-16 12:59:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna |2013-10-16 12:59:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna |2013-10-16 12:59:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna.bnk |2013-10-16 12:59:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna.bnk |2013-10-16 12:59:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa |2013-10-16 12:59:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa |2013-10-16 12:59:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa.bnk |2013-10-16 12:59:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa.bnk |2013-10-16 12:59:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.cvg |2013-10-16 12:59:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.cvg |2013-10-16 12:59:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.map |2013-10-16 12:59:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.gene.map |2013-10-16 12:59:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.faa |2013-10-16 12:59:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.fna |2013-10-16 12:59:58| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.41.asm.contig |2013-10-16 12:59:58| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:00:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.prokka --prefix velvet-sc.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.41.asm.contig |2013-10-16 13:00:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.prokka/velvet-sc.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.ctg.fna |2013-10-16 13:00:40| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.prokka/velvet-sc.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.ctg.faa |2013-10-16 13:00:40| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.ctg.gene.cvg |2013-10-16 13:00:40| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.ctg.gene.map |2013-10-16 13:00:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna |2013-10-16 13:00:40| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna |2013-10-16 13:00:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna.bnk |2013-10-16 13:00:41| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna.bnk |2013-10-16 13:00:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa |2013-10-16 13:00:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa |2013-10-16 13:00:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa.bnk |2013-10-16 13:00:41| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa.bnk |2013-10-16 13:00:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.cvg |2013-10-16 13:00:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.cvg |2013-10-16 13:00:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.map |2013-10-16 13:00:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.gene.map |2013-10-16 13:00:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.faa |2013-10-16 13:00:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.fna |2013-10-16 13:00:42| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.45.asm.contig |2013-10-16 13:00:42| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:01:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.prokka --prefix velvet-sc.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.45.asm.contig |2013-10-16 13:01:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.prokka/velvet-sc.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.ctg.fna |2013-10-16 13:01:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.prokka/velvet-sc.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.ctg.faa |2013-10-16 13:01:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.ctg.gene.cvg |2013-10-16 13:01:24| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.ctg.gene.map |2013-10-16 13:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna |2013-10-16 13:01:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna |2013-10-16 13:01:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna.bnk |2013-10-16 13:01:25| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna.bnk |2013-10-16 13:01:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa |2013-10-16 13:01:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa |2013-10-16 13:01:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa.bnk |2013-10-16 13:01:25| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa.bnk |2013-10-16 13:01:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.cvg |2013-10-16 13:01:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.cvg |2013-10-16 13:01:25| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.map |2013-10-16 13:01:25| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.gene.map |2013-10-16 13:01:25| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.faa |2013-10-16 13:01:25| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.fna |2013-10-16 13:01:25| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.55.asm.contig |2013-10-16 13:01:25| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:02:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.prokka --prefix velvet-sc.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.55.asm.contig |2013-10-16 13:02:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.prokka/velvet-sc.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.ctg.fna |2013-10-16 13:02:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.prokka/velvet-sc.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.ctg.faa |2013-10-16 13:02:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.ctg.gene.cvg |2013-10-16 13:02:07| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.ctg.gene.map |2013-10-16 13:02:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna |2013-10-16 13:02:07| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna |2013-10-16 13:02:07| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna.bnk |2013-10-16 13:02:08| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna.bnk |2013-10-16 13:02:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa |2013-10-16 13:02:08| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa |2013-10-16 13:02:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa.bnk |2013-10-16 13:02:08| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa.bnk |2013-10-16 13:02:08| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.cvg |2013-10-16 13:02:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.cvg |2013-10-16 13:02:09| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.map |2013-10-16 13:02:09| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.gene.map |2013-10-16 13:02:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.faa |2013-10-16 13:02:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.fna |2013-10-16 13:02:09| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.65.asm.contig |2013-10-16 13:02:09| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:03:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.prokka --prefix velvet-sc.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.65.asm.contig |2013-10-16 13:03:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.prokka/velvet-sc.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.ctg.fna |2013-10-16 13:03:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.prokka/velvet-sc.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.ctg.faa |2013-10-16 13:03:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.ctg.gene.cvg |2013-10-16 13:03:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.ctg.gene.map |2013-10-16 13:03:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna |2013-10-16 13:03:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna |2013-10-16 13:03:40| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna.bnk |2013-10-16 13:03:41| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna.bnk |2013-10-16 13:03:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa |2013-10-16 13:03:41| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa |2013-10-16 13:03:41| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa.bnk |2013-10-16 13:03:42| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa.bnk |2013-10-16 13:03:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.cvg |2013-10-16 13:03:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.cvg |2013-10-16 13:03:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.map |2013-10-16 13:03:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.gene.map |2013-10-16 13:03:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.faa |2013-10-16 13:03:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.fna |2013-10-16 13:03:42| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.75.asm.contig |2013-10-16 13:03:42| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:04:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.prokka --prefix velvet-sc.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.75.asm.contig |2013-10-16 13:04:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.prokka/velvet-sc.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.ctg.fna |2013-10-16 13:04:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.prokka/velvet-sc.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.ctg.faa |2013-10-16 13:04:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.ctg.gene.cvg |2013-10-16 13:04:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.ctg.gene.map |2013-10-16 13:04:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna |2013-10-16 13:04:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna |2013-10-16 13:04:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna.bnk |2013-10-16 13:04:44| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna.bnk |2013-10-16 13:04:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa |2013-10-16 13:04:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa |2013-10-16 13:04:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa.bnk |2013-10-16 13:04:45| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa.bnk |2013-10-16 13:04:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.cvg |2013-10-16 13:04:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.cvg |2013-10-16 13:04:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.map |2013-10-16 13:04:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.gene.map |2013-10-16 13:04:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.faa |2013-10-16 13:04:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.fna |2013-10-16 13:04:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.85.asm.contig |2013-10-16 13:04:46| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:05:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.prokka --prefix velvet-sc.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.85.asm.contig |2013-10-16 13:05:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.prokka/velvet-sc.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.ctg.fna |2013-10-16 13:05:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.prokka/velvet-sc.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.ctg.faa |2013-10-16 13:05:34| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.ctg.gene.cvg |2013-10-16 13:05:34| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.ctg.gene.map |2013-10-16 13:05:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna |2013-10-16 13:05:34| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna |2013-10-16 13:05:34| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna.bnk |2013-10-16 13:05:35| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna.bnk |2013-10-16 13:05:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa |2013-10-16 13:05:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa |2013-10-16 13:05:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa.bnk |2013-10-16 13:05:35| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa.bnk |2013-10-16 13:05:35| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.cvg |2013-10-16 13:05:35| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.cvg |2013-10-16 13:05:36| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.map |2013-10-16 13:05:36| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.gene.map |2013-10-16 13:05:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.faa |2013-10-16 13:05:36| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.fna |2013-10-16 13:05:36| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.95.asm.contig |2013-10-16 13:05:36| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:06:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.prokka --prefix velvet-sc.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet-sc.95.asm.contig |2013-10-16 13:06:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.prokka/velvet-sc.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.ctg.fna |2013-10-16 13:06:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.prokka/velvet-sc.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.ctg.faa |2013-10-16 13:06:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.ctg.gene.cvg |2013-10-16 13:06:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.ctg.gene.map |2013-10-16 13:06:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna |2013-10-16 13:06:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna |2013-10-16 13:06:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna.bnk |2013-10-16 13:06:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna.bnk |2013-10-16 13:06:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa |2013-10-16 13:06:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa |2013-10-16 13:06:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa.bnk |2013-10-16 13:06:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa.bnk |2013-10-16 13:06:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.cvg |2013-10-16 13:06:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.cvg |2013-10-16 13:06:22| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.map |2013-10-16 13:06:22| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.gene.map |2013-10-16 13:06:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.faa |2013-10-16 13:06:22| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet-sc.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.fna |2013-10-16 13:06:22| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.105.asm.contig |2013-10-16 13:06:22| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:07:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.prokka --prefix velvet.105 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.105.asm.contig |2013-10-16 13:07:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.prokka/velvet.105.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.ctg.fna |2013-10-16 13:07:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.prokka/velvet.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.ctg.faa |2013-10-16 13:07:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.ctg.gene.cvg |2013-10-16 13:07:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.ctg.gene.map |2013-10-16 13:07:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna |2013-10-16 13:07:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna |2013-10-16 13:07:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna.bnk |2013-10-16 13:07:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna.bnk |2013-10-16 13:07:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa |2013-10-16 13:07:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa |2013-10-16 13:07:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa.bnk |2013-10-16 13:07:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa.bnk |2013-10-16 13:07:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.cvg |2013-10-16 13:07:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.cvg |2013-10-16 13:07:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.map |2013-10-16 13:07:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.gene.map |2013-10-16 13:07:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.faa |2013-10-16 13:07:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.105.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.fna |2013-10-16 13:07:02| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.125.asm.contig |2013-10-16 13:07:02| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-16 13:07:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.prokka --prefix velvet.125 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.125.asm.contig |2013-10-16 13:07:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.prokka/velvet.125.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.ctg.fna |2013-10-16 13:07:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.prokka/velvet.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.ctg.faa |2013-10-16 13:07:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.ctg.gene.cvg |2013-10-16 13:07:45| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.ctg.gene.map |2013-10-16 13:07:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna |2013-10-16 13:07:45| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna |2013-10-16 13:07:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna.bnk |2013-10-16 13:07:45| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna.bnk |2013-10-16 13:07:45| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa |2013-10-16 13:07:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa |2013-10-16 13:07:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa.bnk |2013-10-16 13:07:46| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa.bnk |2013-10-16 13:07:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.cvg |2013-10-16 13:07:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.cvg |2013-10-16 13:07:46| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.map |2013-10-16 13:07:46| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.gene.map |2013-10-16 13:07:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.faa |2013-10-16 13:07:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.125.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.fna |2013-10-16 13:07:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.25.asm.contig |2013-10-16 13:07:46| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:54:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.prokka --prefix velvet.25 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.25.asm.contig |2013-10-17 00:54:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.prokka/velvet.25.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.ctg.fna |2013-10-17 00:54:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.prokka/velvet.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.ctg.faa |2013-10-17 00:54:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.ctg.gene.cvg |2013-10-17 00:54:43| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.ctg.gene.map |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna |2013-10-17 00:54:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna.bnk |2013-10-17 00:54:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna.bnk |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa |2013-10-17 00:54:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa.bnk |2013-10-17 00:54:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa.bnk |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.cvg |2013-10-17 00:54:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.cvg |2013-10-17 00:54:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.map |2013-10-17 00:54:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.gene.map |2013-10-17 00:54:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.faa |2013-10-17 00:54:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.25.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.fna |2013-10-17 00:54:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.35.asm.contig |2013-10-17 00:54:44| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:55:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.prokka --prefix velvet.35 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.35.asm.contig |2013-10-17 00:55:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.prokka/velvet.35.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.ctg.fna |2013-10-17 00:55:32| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.prokka/velvet.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.ctg.faa |2013-10-17 00:55:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.ctg.gene.cvg |2013-10-17 00:55:32| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.ctg.gene.map |2013-10-17 00:55:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna |2013-10-17 00:55:32| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna |2013-10-17 00:55:32| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna.bnk |2013-10-17 00:55:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna.bnk |2013-10-17 00:55:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa |2013-10-17 00:55:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa |2013-10-17 00:55:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa.bnk |2013-10-17 00:55:33| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa.bnk |2013-10-17 00:55:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.cvg |2013-10-17 00:55:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.cvg |2013-10-17 00:55:33| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.map |2013-10-17 00:55:33| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.gene.map |2013-10-17 00:55:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.faa |2013-10-17 00:55:33| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.35.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.fna |2013-10-17 00:55:33| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.41.asm.contig |2013-10-17 00:55:33| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:56:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.prokka --prefix velvet.41 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.41.asm.contig |2013-10-17 00:56:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.prokka/velvet.41.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.ctg.fna |2013-10-17 00:56:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.prokka/velvet.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.ctg.faa |2013-10-17 00:56:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.ctg.gene.cvg |2013-10-17 00:56:13| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.ctg.gene.map |2013-10-17 00:56:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna |2013-10-17 00:56:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna |2013-10-17 00:56:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna.bnk |2013-10-17 00:56:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna.bnk |2013-10-17 00:56:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa |2013-10-17 00:56:14| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa |2013-10-17 00:56:14| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa.bnk |2013-10-17 00:56:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa.bnk |2013-10-17 00:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.cvg |2013-10-17 00:56:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.cvg |2013-10-17 00:56:15| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.map |2013-10-17 00:56:15| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.gene.map |2013-10-17 00:56:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.faa |2013-10-17 00:56:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.41.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.fna |2013-10-17 00:56:15| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.45.asm.contig |2013-10-17 00:56:15| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:56:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.prokka --prefix velvet.45 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.45.asm.contig |2013-10-17 00:56:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.prokka/velvet.45.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.ctg.fna |2013-10-17 00:56:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.prokka/velvet.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.ctg.faa |2013-10-17 00:56:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.ctg.gene.cvg |2013-10-17 00:56:56| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.ctg.gene.map |2013-10-17 00:56:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna |2013-10-17 00:56:56| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna |2013-10-17 00:56:56| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna.bnk |2013-10-17 00:56:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna.bnk |2013-10-17 00:56:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa |2013-10-17 00:56:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa |2013-10-17 00:56:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa.bnk |2013-10-17 00:56:57| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa.bnk |2013-10-17 00:56:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.cvg |2013-10-17 00:56:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.cvg |2013-10-17 00:56:57| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.map |2013-10-17 00:56:57| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.gene.map |2013-10-17 00:56:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.faa |2013-10-17 00:56:57| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.45.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.fna |2013-10-17 00:56:57| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.55.asm.contig |2013-10-17 00:56:57| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:57:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.prokka --prefix velvet.55 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.55.asm.contig |2013-10-17 00:57:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.prokka/velvet.55.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.ctg.fna |2013-10-17 00:57:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.prokka/velvet.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.ctg.faa |2013-10-17 00:57:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.ctg.gene.cvg |2013-10-17 00:57:37| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.ctg.gene.map |2013-10-17 00:57:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna |2013-10-17 00:57:37| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna |2013-10-17 00:57:37| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna.bnk |2013-10-17 00:57:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna.bnk |2013-10-17 00:57:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa |2013-10-17 00:57:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa |2013-10-17 00:57:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa.bnk |2013-10-17 00:57:38| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa.bnk |2013-10-17 00:57:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.cvg |2013-10-17 00:57:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.cvg |2013-10-17 00:57:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.map |2013-10-17 00:57:38| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.gene.map |2013-10-17 00:57:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.faa |2013-10-17 00:57:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.55.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.fna |2013-10-17 00:57:38| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.65.asm.contig |2013-10-17 00:57:38| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:58:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.prokka --prefix velvet.65 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.65.asm.contig |2013-10-17 00:58:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.prokka/velvet.65.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.ctg.fna |2013-10-17 00:58:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.prokka/velvet.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.ctg.faa |2013-10-17 00:58:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.ctg.gene.cvg |2013-10-17 00:58:20| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.ctg.gene.map |2013-10-17 00:58:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna |2013-10-17 00:58:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna |2013-10-17 00:58:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna.bnk |2013-10-17 00:58:20| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna.bnk |2013-10-17 00:58:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa |2013-10-17 00:58:20| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa |2013-10-17 00:58:20| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa.bnk |2013-10-17 00:58:21| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa.bnk |2013-10-17 00:58:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.cvg |2013-10-17 00:58:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.cvg |2013-10-17 00:58:21| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.map |2013-10-17 00:58:21| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.gene.map |2013-10-17 00:58:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.faa |2013-10-17 00:58:21| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.65.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.fna |2013-10-17 00:58:21| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.75.asm.contig |2013-10-17 00:58:21| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:59:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.prokka --prefix velvet.75 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.75.asm.contig |2013-10-17 00:59:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.prokka/velvet.75.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.ctg.fna |2013-10-17 00:59:01| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.prokka/velvet.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.ctg.faa |2013-10-17 00:59:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.ctg.gene.cvg |2013-10-17 00:59:01| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.ctg.gene.map |2013-10-17 00:59:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna |2013-10-17 00:59:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna |2013-10-17 00:59:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna.bnk |2013-10-17 00:59:01| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna.bnk |2013-10-17 00:59:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa |2013-10-17 00:59:01| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa |2013-10-17 00:59:01| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa.bnk |2013-10-17 00:59:02| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa.bnk |2013-10-17 00:59:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.cvg |2013-10-17 00:59:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.cvg |2013-10-17 00:59:02| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.map |2013-10-17 00:59:02| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.gene.map |2013-10-17 00:59:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.faa |2013-10-17 00:59:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.75.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.fna |2013-10-17 00:59:02| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.85.asm.contig |2013-10-17 00:59:02| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 00:59:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.prokka --prefix velvet.85 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.85.asm.contig |2013-10-17 00:59:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.prokka/velvet.85.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.ctg.fna |2013-10-17 00:59:42| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.prokka/velvet.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.ctg.faa |2013-10-17 00:59:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.ctg.gene.cvg |2013-10-17 00:59:42| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.ctg.gene.map |2013-10-17 00:59:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna |2013-10-17 00:59:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna |2013-10-17 00:59:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna.bnk |2013-10-17 00:59:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna.bnk |2013-10-17 00:59:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa |2013-10-17 00:59:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa |2013-10-17 00:59:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa.bnk |2013-10-17 00:59:43| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa.bnk |2013-10-17 00:59:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.cvg |2013-10-17 00:59:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.cvg |2013-10-17 00:59:43| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.map |2013-10-17 00:59:43| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.gene.map |2013-10-17 00:59:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.faa |2013-10-17 00:59:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.85.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.fna |2013-10-17 00:59:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.95.asm.contig |2013-10-17 00:59:43| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/ |2013-10-17 01:00:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.prokka --prefix velvet.95 --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/velvet.95.asm.contig |2013-10-17 01:00:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.prokka/velvet.95.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.ctg.fna |2013-10-17 01:00:23| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.prokka/velvet.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.ctg.faa |2013-10-17 01:00:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.ctg.gene.cvg |2013-10-17 01:00:23| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.ctg.gene.map |2013-10-17 01:00:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna |2013-10-17 01:00:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna |2013-10-17 01:00:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna.bnk |2013-10-17 01:00:23| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna.bnk |2013-10-17 01:00:23| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa |2013-10-17 01:00:23| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa |2013-10-17 01:00:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa.bnk |2013-10-17 01:00:24| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa.bnk |2013-10-17 01:00:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.cvg |2013-10-17 01:00:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.cvg |2013-10-17 01:00:24| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.map |2013-10-17 01:00:24| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.gene.map |2013-10-17 01:00:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.faa |2013-10-17 01:00:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/velvet.95.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.fna |2013-10-17 01:00:28|# [VALIDATE] |2013-10-17 01:03:06| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.25.sam -p 16 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.prob |2013-10-17 01:04:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.bam |2013-10-17 01:06:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted |2013-10-17 01:06:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam |2013-10-17 01:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.25 |2013-10-17 01:07:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 |2013-10-17 01:11:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig 100 16 |2013-10-17 01:12:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.cgal |2013-10-17 01:15:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig abyss.25.ale |2013-10-17 01:15:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig |2013-10-21 11:50:01|# [VALIDATE] |2013-10-21 11:52:39| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.prob |2013-10-21 11:54:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.bam |2013-10-21 11:55:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted |2013-10-21 11:55:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam |2013-10-21 11:56:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.25 |2013-10-21 11:56:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 |2013-10-21 11:59:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig 100 32 |2013-10-21 12:00:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.cgal |2013-10-21 12:03:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig abyss.25.ale |2013-10-21 12:15:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig |2013-10-21 12:15:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr |2013-10-21 12:15:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.cmds |2013-10-21 12:15:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.fa |2013-10-21 12:16:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 12:18:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.raw.bam |2013-10-21 12:19:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.raw.bam.sort |2013-10-21 12:20:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.rmdup.bam |2013-10-21 12:20:28| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.header |2013-10-21 12:20:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.header |2013-10-21 12:20:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam |2013-10-21 12:20:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam |2013-10-21 12:20:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.bam.tmp.7526.smaltmap.* |2013-10-21 12:21:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.perfect |2013-10-21 12:21:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr.sam.sorted.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.25.reapr |2013-10-21 13:09:12|# [VALIDATE] |2013-10-21 13:11:40| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.prob |2013-10-21 13:13:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.bam |2013-10-21 13:14:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.sorted |2013-10-21 13:14:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.sorted.bam |2013-10-21 13:15:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.35 |2013-10-21 13:15:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0 |2013-10-21 13:18:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig 100 32 |2013-10-21 13:19:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.cgal |2013-10-21 13:22:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig abyss.35.ale |2013-10-21 13:34:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig |2013-10-21 13:34:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr |2013-10-21 13:34:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.cmds |2013-10-21 13:34:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.fa |2013-10-21 13:34:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 13:36:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.raw.bam |2013-10-21 13:38:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.raw.bam.sort |2013-10-21 13:39:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.rmdup.bam |2013-10-21 13:39:11| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.header |2013-10-21 13:39:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.header |2013-10-21 13:39:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam |2013-10-21 13:39:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam |2013-10-21 13:39:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam.tmp.17281.smaltmap.* |2013-10-21 13:39:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.perfect |2013-10-21 13:50:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.35.reapr |2013-10-21 13:52:35| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.prob |2013-10-21 13:54:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.bam |2013-10-21 13:55:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.sorted |2013-10-21 13:55:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.sorted.bam |2013-10-21 13:56:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.41 |2013-10-21 13:56:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0 |2013-10-21 13:59:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig 100 32 |2013-10-21 14:00:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.cgal |2013-10-21 14:03:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig abyss.41.ale |2013-10-21 14:15:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig |2013-10-21 14:15:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr |2013-10-21 14:15:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.cmds |2013-10-21 14:15:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.fa |2013-10-21 14:16:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 14:20:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.raw.bam |2013-10-21 14:21:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.raw.bam.sort |2013-10-21 14:22:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.rmdup.bam |2013-10-21 14:22:51| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.header |2013-10-21 14:22:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.header |2013-10-21 14:22:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam |2013-10-21 14:22:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam |2013-10-21 14:22:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam.tmp.22697.smaltmap.* |2013-10-21 14:23:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.perfect |2013-10-21 14:33:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.41.reapr |2013-10-21 14:36:54| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.prob |2013-10-21 14:38:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.bam |2013-10-21 14:40:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.sorted |2013-10-21 14:40:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.sorted.bam |2013-10-21 14:40:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.45 |2013-10-21 14:41:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0 |2013-10-21 14:43:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig 100 32 |2013-10-21 14:45:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.cgal |2013-10-21 14:48:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig abyss.45.ale |2013-10-21 15:00:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig |2013-10-21 15:00:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr |2013-10-21 15:00:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.cmds |2013-10-21 15:00:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.fa |2013-10-21 15:00:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 15:04:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.raw.bam |2013-10-21 15:05:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.raw.bam.sort |2013-10-21 15:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.rmdup.bam |2013-10-21 15:06:47| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.header |2013-10-21 15:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.header |2013-10-21 15:06:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam |2013-10-21 15:06:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam |2013-10-21 15:06:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam.tmp.3443.smaltmap.* |2013-10-21 15:07:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.perfect |2013-10-21 15:17:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.45.reapr |2013-10-21 15:20:22| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.prob |2013-10-21 15:21:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.bam |2013-10-21 15:23:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.sorted |2013-10-21 15:23:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.sorted.bam |2013-10-21 15:24:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.55 |2013-10-21 15:24:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0 |2013-10-21 15:26:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig 100 32 |2013-10-21 15:28:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.cgal |2013-10-21 15:31:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig abyss.55.ale |2013-10-21 15:43:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig |2013-10-21 15:43:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr |2013-10-21 15:43:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.cmds |2013-10-21 15:43:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.fa |2013-10-21 15:43:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 15:47:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.raw.bam |2013-10-21 15:48:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.raw.bam.sort |2013-10-21 15:49:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.rmdup.bam |2013-10-21 15:49:44| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.header |2013-10-21 15:49:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.header |2013-10-21 15:49:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam |2013-10-21 15:49:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam |2013-10-21 15:49:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam.tmp.10393.smaltmap.* |2013-10-21 15:50:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.perfect |2013-10-21 16:00:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.55.reapr |2013-10-21 16:02:58| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.prob |2013-10-21 16:04:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.bam |2013-10-21 16:06:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.sorted |2013-10-21 16:06:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.sorted.bam |2013-10-21 16:06:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.65 |2013-10-21 16:07:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0 |2013-10-21 16:09:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig 100 32 |2013-10-21 16:10:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.cgal |2013-10-21 16:13:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig abyss.65.ale |2013-10-21 16:25:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig |2013-10-21 16:25:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr |2013-10-21 16:25:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.cmds |2013-10-21 16:25:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.fa |2013-10-21 16:25:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 16:29:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.raw.bam |2013-10-21 16:31:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.raw.bam.sort |2013-10-21 16:32:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.rmdup.bam |2013-10-21 16:32:07| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.header |2013-10-21 16:32:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.header |2013-10-21 16:32:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam |2013-10-21 16:32:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam |2013-10-21 16:32:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam.tmp.15631.smaltmap.* |2013-10-21 16:32:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.perfect |2013-10-21 16:42:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.65.reapr |2013-10-21 16:45:07| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.prob |2013-10-21 16:46:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.bam |2013-10-21 16:48:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.sorted |2013-10-21 16:48:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.sorted.bam |2013-10-21 16:48:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.75 |2013-10-21 16:49:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0 |2013-10-21 16:51:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig 100 32 |2013-10-21 16:52:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.cgal |2013-10-21 16:56:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig abyss.75.ale |2013-10-21 17:07:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig |2013-10-21 17:07:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr |2013-10-21 17:07:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.cmds |2013-10-21 17:07:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.fa |2013-10-21 17:07:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 17:09:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.raw.bam |2013-10-21 17:11:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.raw.bam.sort |2013-10-21 17:12:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.rmdup.bam |2013-10-21 17:12:12| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.header |2013-10-21 17:12:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.header |2013-10-21 17:12:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam |2013-10-21 17:12:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam |2013-10-21 17:12:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam.tmp.20782.smaltmap.* |2013-10-21 17:12:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.perfect |2013-10-21 17:22:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.75.reapr |2013-10-21 17:24:51| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.prob |2013-10-21 17:26:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.bam |2013-10-21 17:27:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.sorted |2013-10-21 17:28:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.sorted.bam |2013-10-21 17:28:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.85 |2013-10-21 17:29:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0 |2013-10-21 17:31:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig 100 32 |2013-10-21 17:32:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.cgal |2013-10-21 17:35:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig abyss.85.ale |2013-10-21 17:47:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig |2013-10-21 17:47:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr |2013-10-21 17:47:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.cmds |2013-10-21 17:47:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.fa |2013-10-21 17:47:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 17:49:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.raw.bam |2013-10-21 17:50:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.raw.bam.sort |2013-10-21 17:51:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.rmdup.bam |2013-10-21 17:51:40| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.header |2013-10-21 17:51:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.header |2013-10-21 17:51:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam |2013-10-21 17:51:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam |2013-10-21 17:51:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam.tmp.25775.smaltmap.* |2013-10-21 17:52:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.perfect |2013-10-21 18:01:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.85.reapr |2013-10-21 18:03:33| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file abyss.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.prob |2013-10-21 18:04:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.bam |2013-10-21 18:06:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.sorted |2013-10-21 18:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.sorted.bam |2013-10-21 18:07:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_abyss.95 |2013-10-21 18:07:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0 |2013-10-21 18:09:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig 100 32 |2013-10-21 18:11:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.cgal |2013-10-21 18:14:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig abyss.95.ale |2013-10-21 18:25:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig |2013-10-21 18:25:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr |2013-10-21 18:25:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.cmds |2013-10-21 18:25:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.fa |2013-10-21 18:25:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 18:27:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.raw.bam |2013-10-21 18:28:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.raw.bam.sort |2013-10-21 18:29:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.rmdup.bam |2013-10-21 18:29:57| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.header |2013-10-21 18:29:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.header |2013-10-21 18:29:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam |2013-10-21 18:30:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam |2013-10-21 18:30:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam.tmp.30813.smaltmap.* |2013-10-21 18:30:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.perfect |2013-10-21 18:39:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/abyss.95.reapr |2013-10-21 18:41:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.prob |2013-10-21 18:42:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.bam |2013-10-21 18:44:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.sorted |2013-10-21 18:44:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.sorted.bam |2013-10-21 18:44:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.105 |2013-10-21 18:45:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0 |2013-10-21 18:47:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig 100 32 |2013-10-21 18:49:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.cgal |2013-10-21 18:52:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig idba-ud.105.ale |2013-10-21 19:03:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig |2013-10-21 19:03:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr |2013-10-21 19:03:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.cmds |2013-10-21 19:03:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.fa |2013-10-21 19:03:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 19:05:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.raw.bam |2013-10-21 19:07:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.raw.bam.sort |2013-10-21 19:08:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.rmdup.bam |2013-10-21 19:08:19| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.header |2013-10-21 19:08:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.header |2013-10-21 19:08:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam |2013-10-21 19:08:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam |2013-10-21 19:08:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam.tmp.3413.smaltmap.* |2013-10-21 19:08:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.perfect |2013-10-21 19:19:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.105.reapr |2013-10-21 19:21:31| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.prob |2013-10-21 19:22:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.bam |2013-10-21 19:24:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.sorted |2013-10-21 19:24:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.sorted.bam |2013-10-21 19:24:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.25 |2013-10-21 19:25:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0 |2013-10-21 19:27:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig 100 32 |2013-10-21 19:28:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.cgal |2013-10-21 19:31:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig idba-ud.25.ale |2013-10-21 19:40:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig |2013-10-21 19:40:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr |2013-10-21 19:40:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.cmds |2013-10-21 19:40:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.fa |2013-10-21 19:40:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 19:43:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.raw.bam |2013-10-21 19:45:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.raw.bam.sort |2013-10-21 19:46:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.rmdup.bam |2013-10-21 19:46:00| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.header |2013-10-21 19:46:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.header |2013-10-21 19:46:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam |2013-10-21 19:46:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam |2013-10-21 19:46:06| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam.tmp.8075.smaltmap.* |2013-10-21 19:46:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.perfect |2013-10-21 19:56:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.25.reapr |2013-10-21 19:58:48| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.prob |2013-10-21 20:00:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.bam |2013-10-21 20:01:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.sorted |2013-10-21 20:01:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.sorted.bam |2013-10-21 20:02:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.35 |2013-10-21 20:02:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0 |2013-10-21 20:05:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig 100 32 |2013-10-21 20:06:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.cgal |2013-10-21 20:09:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig idba-ud.35.ale |2013-10-21 20:18:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig |2013-10-21 20:18:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr |2013-10-21 20:18:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.cmds |2013-10-21 20:19:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.fa |2013-10-21 20:19:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 20:22:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.raw.bam |2013-10-21 20:23:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.raw.bam.sort |2013-10-21 20:24:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.rmdup.bam |2013-10-21 20:24:51| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.header |2013-10-21 20:24:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.header |2013-10-21 20:24:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam |2013-10-21 20:24:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam |2013-10-21 20:24:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam.tmp.13160.smaltmap.* |2013-10-21 20:25:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.perfect |2013-10-21 20:36:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.35.reapr |2013-10-21 20:38:56| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.prob |2013-10-21 20:40:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.bam |2013-10-21 20:41:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.sorted |2013-10-21 20:41:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.sorted.bam |2013-10-21 20:42:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.41 |2013-10-21 20:42:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0 |2013-10-21 20:45:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig 100 32 |2013-10-21 20:46:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.cgal |2013-10-21 20:49:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig idba-ud.41.ale |2013-10-21 20:59:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig |2013-10-21 20:59:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr |2013-10-21 20:59:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.cmds |2013-10-21 20:59:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.fa |2013-10-21 21:00:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 21:03:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.raw.bam |2013-10-21 21:04:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.raw.bam.sort |2013-10-21 21:05:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.rmdup.bam |2013-10-21 21:05:33| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.header |2013-10-21 21:05:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.header |2013-10-21 21:05:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam |2013-10-21 21:05:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam |2013-10-21 21:05:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam.tmp.18477.smaltmap.* |2013-10-21 21:06:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.perfect |2013-10-21 21:17:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.41.reapr |2013-10-21 21:20:08| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.prob |2013-10-21 21:21:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.bam |2013-10-21 21:23:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.sorted |2013-10-21 21:23:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.sorted.bam |2013-10-21 21:23:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.45 |2013-10-21 21:24:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0 |2013-10-21 21:26:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig 100 32 |2013-10-21 21:28:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.cgal |2013-10-21 21:31:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig idba-ud.45.ale |2013-10-21 21:40:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig |2013-10-21 21:40:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr |2013-10-21 21:40:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.cmds |2013-10-21 21:41:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.fa |2013-10-21 21:41:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 21:44:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.raw.bam |2013-10-21 21:45:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.raw.bam.sort |2013-10-21 21:46:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.rmdup.bam |2013-10-21 21:46:55| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.header |2013-10-21 21:46:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.header |2013-10-21 21:46:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam |2013-10-21 21:47:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam |2013-10-21 21:47:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam.tmp.23592.smaltmap.* |2013-10-21 21:47:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.perfect |2013-10-21 22:00:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.45.reapr |2013-10-21 22:02:44| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.prob |2013-10-21 22:04:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.bam |2013-10-21 22:05:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.sorted |2013-10-21 22:05:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.sorted.bam |2013-10-21 22:06:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.55 |2013-10-21 22:06:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0 |2013-10-21 22:09:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig 100 32 |2013-10-21 22:10:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.cgal |2013-10-21 22:13:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig idba-ud.55.ale |2013-10-21 22:23:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig |2013-10-21 22:23:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr |2013-10-21 22:23:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.cmds |2013-10-21 22:23:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.fa |2013-10-21 22:24:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-21 22:26:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.raw.bam |2013-10-21 22:28:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.raw.bam.sort |2013-10-21 22:29:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.rmdup.bam |2013-10-21 22:29:05| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.header |2013-10-21 22:29:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.header |2013-10-21 22:29:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam |2013-10-21 22:29:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam |2013-10-21 22:29:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam.tmp.28803.smaltmap.* |2013-10-21 22:29:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.perfect |2013-10-21 22:39:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.55.reapr |2013-10-21 22:41:45| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.prob |2013-10-21 22:43:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam |2013-10-21 22:44:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted |2013-10-21 22:44:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam |2013-10-21 22:45:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.65 |2013-10-21 22:45:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 |2013-10-21 22:48:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig 100 32 |2013-10-21 22:49:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.cgal |2013-10-21 22:52:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig idba-ud.65.ale |2013-10-22 10:05:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig |2013-10-22 10:50:33|# [VALIDATE] |2013-10-22 10:53:02| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.prob |2013-10-22 10:54:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam |2013-10-22 10:56:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted |2013-10-22 10:56:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam |2013-10-22 10:56:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.65 |2013-10-22 10:57:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 |2013-10-22 10:59:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig 100 32 |2013-10-22 11:00:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.cgal |2013-10-22 11:03:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig idba-ud.65.ale |2013-10-22 11:03:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig |2013-10-22 11:15:17|# [VALIDATE] |2013-10-22 11:17:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.prob |2013-10-22 11:18:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam |2013-10-22 11:20:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted |2013-10-22 11:20:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam |2013-10-22 11:20:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.65 |2013-10-22 11:21:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 |2013-10-22 11:23:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig 100 32 |2013-10-22 11:25:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.cgal |2013-10-22 11:28:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig idba-ud.65.ale |2013-10-22 11:38:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig |2013-10-22 11:38:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr |2013-10-22 11:38:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.cmds |2013-10-22 11:38:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.fa |2013-10-22 11:39:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 11:41:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.raw.bam |2013-10-22 11:42:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.raw.bam.sort |2013-10-22 11:43:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.rmdup.bam |2013-10-22 11:43:38| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.header |2013-10-22 11:43:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.header |2013-10-22 11:43:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam |2013-10-22 11:43:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam |2013-10-22 11:43:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam.tmp.30334.smaltmap.* |2013-10-22 11:44:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.perfect |2013-10-22 11:54:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.65.reapr |2013-10-22 11:56:40| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.prob |2013-10-22 11:58:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.bam |2013-10-22 11:59:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.sorted |2013-10-22 11:59:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.sorted.bam |2013-10-22 12:00:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.75 |2013-10-22 12:00:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0 |2013-10-22 12:03:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig 100 32 |2013-10-22 12:04:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.cgal |2013-10-22 12:07:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig idba-ud.75.ale |2013-10-22 12:18:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig |2013-10-22 12:18:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr |2013-10-22 12:18:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.cmds |2013-10-22 12:18:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.fa |2013-10-22 12:18:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 12:20:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.raw.bam |2013-10-22 12:22:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.raw.bam.sort |2013-10-22 12:23:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.rmdup.bam |2013-10-22 12:23:01| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.header |2013-10-22 12:23:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.header |2013-10-22 12:23:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam |2013-10-22 12:23:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam |2013-10-22 12:23:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam.tmp.3136.smaltmap.* |2013-10-22 12:23:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.perfect |2013-10-22 12:34:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.75.reapr |2013-10-22 12:37:21| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.prob |2013-10-22 12:38:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.bam |2013-10-22 12:40:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.sorted |2013-10-22 12:40:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.sorted.bam |2013-10-22 12:40:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.85 |2013-10-22 12:41:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0 |2013-10-22 12:43:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig 100 32 |2013-10-22 12:45:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.cgal |2013-10-22 12:48:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig idba-ud.85.ale |2013-10-22 12:59:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig |2013-10-22 12:59:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr |2013-10-22 12:59:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.cmds |2013-10-22 12:59:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.fa |2013-10-22 12:59:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 13:03:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.raw.bam |2013-10-22 13:05:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.raw.bam.sort |2013-10-22 13:06:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.rmdup.bam |2013-10-22 13:06:27| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.header |2013-10-22 13:06:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.header |2013-10-22 13:06:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam |2013-10-22 13:06:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam |2013-10-22 13:06:35| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam.tmp.7522.smaltmap.* |2013-10-22 13:07:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.perfect |2013-10-22 13:21:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.85.reapr |2013-10-22 13:27:30| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file idba-ud.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.prob |2013-10-22 13:28:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.bam |2013-10-22 13:30:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.sorted |2013-10-22 13:30:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.sorted.bam |2013-10-22 13:31:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_idba-ud.95 |2013-10-22 13:31:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0 |2013-10-22 13:33:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig 100 32 |2013-10-22 13:35:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.cgal |2013-10-22 13:38:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig idba-ud.95.ale |2013-10-22 13:53:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig |2013-10-22 13:53:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr |2013-10-22 13:53:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.cmds |2013-10-22 13:53:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.fa |2013-10-22 13:53:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 13:55:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.raw.bam |2013-10-22 13:57:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.raw.bam.sort |2013-10-22 13:58:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.rmdup.bam |2013-10-22 13:58:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.header |2013-10-22 13:58:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.header |2013-10-22 13:58:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam |2013-10-22 13:58:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam |2013-10-22 13:58:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam.tmp.12221.smaltmap.* |2013-10-22 13:59:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.perfect |2013-10-22 14:11:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/idba-ud.95.reapr |2013-10-22 14:17:47| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.prob |2013-10-22 14:19:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.bam |2013-10-22 14:21:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.sorted |2013-10-22 14:21:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.sorted.bam |2013-10-22 14:21:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.105 |2013-10-22 14:22:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0 |2013-10-22 14:24:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig 100 32 |2013-10-22 14:25:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.cgal |2013-10-22 14:28:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig masurca.105.ale |2013-10-22 14:38:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig |2013-10-22 14:38:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr |2013-10-22 14:38:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.cmds |2013-10-22 14:38:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.fa |2013-10-22 14:39:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 14:41:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.raw.bam |2013-10-22 14:42:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.raw.bam.sort |2013-10-22 14:43:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.rmdup.bam |2013-10-22 14:43:53| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.header |2013-10-22 14:43:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.header |2013-10-22 14:43:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam |2013-10-22 14:44:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam |2013-10-22 14:44:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam.tmp.16036.smaltmap.* |2013-10-22 14:44:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.perfect |2013-10-22 14:54:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.105.reapr |2013-10-22 14:56:52| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.prob |2013-10-22 14:58:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.bam |2013-10-22 14:59:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.sorted |2013-10-22 14:59:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.sorted.bam |2013-10-22 15:00:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.125 |2013-10-22 15:00:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0 |2013-10-22 15:02:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig 100 32 |2013-10-22 15:04:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.cgal |2013-10-22 15:07:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig masurca.125.ale |2013-10-22 15:17:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig |2013-10-22 15:17:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr |2013-10-22 15:17:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.cmds |2013-10-22 15:17:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.fa |2013-10-22 15:17:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 15:20:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.raw.bam |2013-10-22 15:21:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.raw.bam.sort |2013-10-22 15:22:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.rmdup.bam |2013-10-22 15:22:38| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.header |2013-10-22 15:22:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.header |2013-10-22 15:22:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam |2013-10-22 15:22:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam |2013-10-22 15:22:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam.tmp.19457.smaltmap.* |2013-10-22 15:23:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.perfect |2013-10-22 15:33:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.125.reapr |2013-10-22 15:36:39| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.prob |2013-10-22 15:38:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.bam |2013-10-22 15:39:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.sorted |2013-10-22 15:39:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.sorted.bam |2013-10-22 15:40:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.25 |2013-10-22 15:40:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0 |2013-10-22 15:43:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig 100 32 |2013-10-22 15:44:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.cgal |2013-10-22 15:47:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig masurca.25.ale |2013-10-22 15:58:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig |2013-10-22 15:58:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr |2013-10-22 15:58:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.cmds |2013-10-22 15:58:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.fa |2013-10-22 15:58:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 16:03:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.raw.bam |2013-10-22 16:05:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.raw.bam.sort |2013-10-22 16:06:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.rmdup.bam |2013-10-22 16:06:12| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.header |2013-10-22 16:06:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.header |2013-10-22 16:06:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam |2013-10-22 16:06:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam |2013-10-22 16:06:18| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam.tmp.22863.smaltmap.* |2013-10-22 16:06:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.perfect |2013-10-22 16:17:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.25.reapr |2013-10-22 16:19:43| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.prob |2013-10-22 16:21:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.bam |2013-10-22 16:22:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.sorted |2013-10-22 16:22:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.sorted.bam |2013-10-22 16:23:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.35 |2013-10-22 16:23:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0 |2013-10-22 16:25:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig 100 32 |2013-10-22 16:27:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.cgal |2013-10-22 16:30:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig masurca.35.ale |2013-10-22 16:40:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig |2013-10-22 16:40:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr |2013-10-22 16:40:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.cmds |2013-10-22 16:40:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.fa |2013-10-22 16:40:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 16:43:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.raw.bam |2013-10-22 16:44:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.raw.bam.sort |2013-10-22 16:45:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.rmdup.bam |2013-10-22 16:45:56| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.header |2013-10-22 16:45:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.header |2013-10-22 16:45:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam |2013-10-22 16:46:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam |2013-10-22 16:46:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam.tmp.26290.smaltmap.* |2013-10-22 16:46:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.perfect |2013-10-22 16:57:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.35.reapr |2013-10-22 16:59:27| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.prob |2013-10-22 17:00:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.bam |2013-10-22 17:02:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.sorted |2013-10-22 17:02:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.sorted.bam |2013-10-22 17:03:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.41 |2013-10-22 17:03:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0 |2013-10-22 17:05:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig 100 32 |2013-10-22 17:06:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.cgal |2013-10-22 17:09:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig masurca.41.ale |2013-10-22 17:20:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig |2013-10-22 17:20:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr |2013-10-22 17:20:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.cmds |2013-10-22 17:20:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.fa |2013-10-22 17:20:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 17:23:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.raw.bam |2013-10-22 17:24:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.raw.bam.sort |2013-10-22 17:25:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.rmdup.bam |2013-10-22 17:25:26| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.header |2013-10-22 17:25:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.header |2013-10-22 17:25:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam |2013-10-22 17:25:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam |2013-10-22 17:25:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam.tmp.29605.smaltmap.* |2013-10-22 17:26:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.perfect |2013-10-22 17:36:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.41.reapr |2013-10-22 17:38:58| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.prob |2013-10-22 17:40:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.bam |2013-10-22 17:41:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.sorted |2013-10-22 17:42:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.sorted.bam |2013-10-22 17:42:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.45 |2013-10-22 17:42:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0 |2013-10-22 17:45:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig 100 32 |2013-10-22 17:46:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.cgal |2013-10-22 17:49:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig masurca.45.ale |2013-10-22 17:59:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig |2013-10-22 17:59:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr |2013-10-22 17:59:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.cmds |2013-10-22 17:59:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.fa |2013-10-22 17:59:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 18:02:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.raw.bam |2013-10-22 18:03:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.raw.bam.sort |2013-10-22 18:04:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.rmdup.bam |2013-10-22 18:04:35| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.header |2013-10-22 18:04:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.header |2013-10-22 18:04:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam |2013-10-22 18:04:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam |2013-10-22 18:04:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam.tmp.302.smaltmap.* |2013-10-22 18:05:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.perfect |2013-10-22 18:15:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.45.reapr |2013-10-22 18:18:18| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.prob |2013-10-22 18:19:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.bam |2013-10-22 18:21:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.sorted |2013-10-22 18:21:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.sorted.bam |2013-10-22 18:21:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.55 |2013-10-22 18:22:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0 |2013-10-22 18:24:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig 100 32 |2013-10-22 18:25:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.cgal |2013-10-22 18:28:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig masurca.55.ale |2013-10-22 18:38:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig |2013-10-22 18:38:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr |2013-10-22 18:38:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.cmds |2013-10-22 18:38:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.fa |2013-10-22 18:39:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 18:41:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.raw.bam |2013-10-22 18:42:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.raw.bam.sort |2013-10-22 18:43:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.rmdup.bam |2013-10-22 18:43:57| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.header |2013-10-22 18:43:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.header |2013-10-22 18:43:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam |2013-10-22 18:44:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam |2013-10-22 18:44:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam.tmp.3519.smaltmap.* |2013-10-22 18:44:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.perfect |2013-10-22 18:55:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.55.reapr |2013-10-22 18:57:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.prob |2013-10-22 18:58:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.bam |2013-10-22 19:00:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.sorted |2013-10-22 19:00:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.sorted.bam |2013-10-22 19:01:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.65 |2013-10-22 19:01:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0 |2013-10-22 19:03:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig 100 32 |2013-10-22 19:04:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.cgal |2013-10-22 19:07:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig masurca.65.ale |2013-10-22 19:17:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig |2013-10-22 19:17:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr |2013-10-22 19:17:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.cmds |2013-10-22 19:18:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.fa |2013-10-22 19:18:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 19:20:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.raw.bam |2013-10-22 19:22:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.raw.bam.sort |2013-10-22 19:23:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.rmdup.bam |2013-10-22 19:23:09| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.header |2013-10-22 19:23:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.header |2013-10-22 19:23:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam |2013-10-22 19:23:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam |2013-10-22 19:23:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam.tmp.6890.smaltmap.* |2013-10-22 19:23:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.perfect |2013-10-22 19:34:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.65.reapr |2013-10-22 19:36:37| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.prob |2013-10-22 19:38:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.bam |2013-10-22 19:39:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.sorted |2013-10-22 19:39:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.sorted.bam |2013-10-22 19:40:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.75 |2013-10-22 19:40:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0 |2013-10-22 19:42:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig 100 32 |2013-10-22 19:43:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.cgal |2013-10-22 19:46:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig masurca.75.ale |2013-10-22 19:56:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig |2013-10-22 19:56:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr |2013-10-22 19:56:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.cmds |2013-10-22 19:56:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.fa |2013-10-22 19:57:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 19:59:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.raw.bam |2013-10-22 20:01:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.raw.bam.sort |2013-10-22 20:02:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.rmdup.bam |2013-10-22 20:02:03| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.header |2013-10-22 20:02:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.header |2013-10-22 20:02:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam |2013-10-22 20:02:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam |2013-10-22 20:02:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam.tmp.10097.smaltmap.* |2013-10-22 20:02:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.perfect |2013-10-22 20:13:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.75.reapr |2013-10-22 20:15:32| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.prob |2013-10-22 20:16:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.bam |2013-10-22 20:18:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.sorted |2013-10-22 20:18:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.sorted.bam |2013-10-22 20:19:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.85 |2013-10-22 20:19:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0 |2013-10-22 20:21:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig 100 32 |2013-10-22 20:22:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.cgal |2013-10-22 20:25:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig masurca.85.ale |2013-10-22 20:35:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig |2013-10-22 20:35:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr |2013-10-22 20:35:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.cmds |2013-10-22 20:35:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.fa |2013-10-22 20:36:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 20:38:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.raw.bam |2013-10-22 20:40:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.raw.bam.sort |2013-10-22 20:41:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.rmdup.bam |2013-10-22 20:41:08| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.header |2013-10-22 20:41:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.header |2013-10-22 20:41:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam |2013-10-22 20:41:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam |2013-10-22 20:41:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam.tmp.13510.smaltmap.* |2013-10-22 20:41:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.perfect |2013-10-22 20:52:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.85.reapr |2013-10-22 20:54:24| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file masurca.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.prob |2013-10-22 20:55:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.bam |2013-10-22 20:57:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.sorted |2013-10-22 20:57:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.sorted.bam |2013-10-22 20:57:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_masurca.95 |2013-10-22 20:58:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0 |2013-10-22 21:00:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig 100 32 |2013-10-22 21:01:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.cgal |2013-10-22 21:04:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig masurca.95.ale |2013-10-22 21:14:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig |2013-10-22 21:14:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr |2013-10-22 21:14:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.cmds |2013-10-22 21:14:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.fa |2013-10-22 21:15:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 21:17:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.raw.bam |2013-10-22 21:19:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.raw.bam.sort |2013-10-22 21:20:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.rmdup.bam |2013-10-22 21:20:02| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.header |2013-10-22 21:20:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.header |2013-10-22 21:20:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam |2013-10-22 21:20:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam |2013-10-22 21:20:08| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam.tmp.16736.smaltmap.* |2013-10-22 21:20:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.perfect |2013-10-22 21:31:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/masurca.95.reapr |2013-10-22 21:33:29| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.prob |2013-10-22 21:34:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.bam |2013-10-22 21:36:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.sorted |2013-10-22 21:36:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.sorted.bam |2013-10-22 21:37:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.105 |2013-10-22 21:37:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0 |2013-10-22 21:39:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig 100 32 |2013-10-22 21:40:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.cgal |2013-10-22 21:44:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig mira.105.ale |2013-10-22 21:55:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig |2013-10-22 21:55:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr |2013-10-22 21:55:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.cmds |2013-10-22 21:55:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.fa |2013-10-22 21:55:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 21:57:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.raw.bam |2013-10-22 21:59:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.raw.bam.sort |2013-10-22 22:00:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.rmdup.bam |2013-10-22 22:00:04| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.header |2013-10-22 22:00:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.header |2013-10-22 22:00:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam |2013-10-22 22:00:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam |2013-10-22 22:00:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam.tmp.19985.smaltmap.* |2013-10-22 22:00:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.perfect |2013-10-22 22:09:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.105.reapr |2013-10-22 22:12:03| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.prob |2013-10-22 22:13:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.bam |2013-10-22 22:15:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.sorted |2013-10-22 22:15:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.sorted.bam |2013-10-22 22:15:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.125 |2013-10-22 22:16:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0 |2013-10-22 22:18:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig 100 32 |2013-10-22 22:19:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.cgal |2013-10-22 22:22:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig mira.125.ale |2013-10-22 22:32:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig |2013-10-22 22:32:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr |2013-10-22 22:32:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.cmds |2013-10-22 22:33:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.fa |2013-10-22 22:33:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 22:34:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.raw.bam |2013-10-22 22:36:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.raw.bam.sort |2013-10-22 22:37:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.rmdup.bam |2013-10-22 22:37:24| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.header |2013-10-22 22:37:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.header |2013-10-22 22:37:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam |2013-10-22 22:37:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam |2013-10-22 22:37:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam.tmp.23461.smaltmap.* |2013-10-22 22:37:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.perfect |2013-10-22 22:46:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.125.reapr |2013-10-22 22:49:09| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.prob |2013-10-22 22:50:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.bam |2013-10-22 22:52:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.sorted |2013-10-22 22:52:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.sorted.bam |2013-10-22 22:52:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.25 |2013-10-22 22:53:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0 |2013-10-22 22:55:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig 100 32 |2013-10-22 22:56:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.cgal |2013-10-22 23:00:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig mira.25.ale |2013-10-22 23:11:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig |2013-10-22 23:11:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr |2013-10-22 23:11:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.cmds |2013-10-22 23:11:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.fa |2013-10-22 23:12:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 23:15:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.raw.bam |2013-10-22 23:16:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.raw.bam.sort |2013-10-22 23:17:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.rmdup.bam |2013-10-22 23:17:39| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.header |2013-10-22 23:17:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.header |2013-10-22 23:17:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam |2013-10-22 23:17:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam |2013-10-22 23:17:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam.tmp.27115.smaltmap.* |2013-10-22 23:18:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.perfect |2013-10-22 23:28:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.25.reapr |2013-10-22 23:31:12| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.prob |2013-10-22 23:32:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.bam |2013-10-22 23:34:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.sorted |2013-10-22 23:34:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.sorted.bam |2013-10-22 23:34:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.35 |2013-10-22 23:35:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0 |2013-10-22 23:37:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig 100 32 |2013-10-22 23:38:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.cgal |2013-10-22 23:42:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig mira.35.ale |2013-10-22 23:53:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig |2013-10-22 23:53:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr |2013-10-22 23:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.cmds |2013-10-22 23:53:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.fa |2013-10-22 23:54:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-22 23:57:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.raw.bam |2013-10-22 23:58:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.raw.bam.sort |2013-10-22 23:59:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.rmdup.bam |2013-10-22 23:59:42| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.header |2013-10-22 23:59:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.header |2013-10-22 23:59:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam |2013-10-22 23:59:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam |2013-10-22 23:59:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam.tmp.30539.smaltmap.* |2013-10-23 00:00:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.perfect |2013-10-23 00:10:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.35.reapr |2013-10-23 00:12:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.prob |2013-10-23 00:14:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.bam |2013-10-23 00:16:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.sorted |2013-10-23 00:16:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.sorted.bam |2013-10-23 00:16:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.41 |2013-10-23 00:17:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0 |2013-10-23 00:19:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig 100 32 |2013-10-23 00:20:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.cgal |2013-10-23 00:23:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig mira.41.ale |2013-10-23 00:35:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig |2013-10-23 00:35:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr |2013-10-23 00:35:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.cmds |2013-10-23 00:35:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.fa |2013-10-23 00:36:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 00:37:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.raw.bam |2013-10-23 00:39:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.raw.bam.sort |2013-10-23 00:40:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.rmdup.bam |2013-10-23 00:40:07| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.header |2013-10-23 00:40:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.header |2013-10-23 00:40:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam |2013-10-23 00:40:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam |2013-10-23 00:40:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam.tmp.1510.smaltmap.* |2013-10-23 00:40:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.perfect |2013-10-23 00:51:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.41.reapr |2013-10-23 00:53:30| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.prob |2013-10-23 00:54:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.bam |2013-10-23 00:56:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.sorted |2013-10-23 00:56:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.sorted.bam |2013-10-23 00:57:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.45 |2013-10-23 00:57:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0 |2013-10-23 00:59:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig 100 32 |2013-10-23 01:01:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.cgal |2013-10-23 01:04:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig mira.45.ale |2013-10-23 01:16:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig |2013-10-23 01:16:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr |2013-10-23 01:16:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.cmds |2013-10-23 01:16:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.fa |2013-10-23 01:16:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 01:18:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.raw.bam |2013-10-23 01:19:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.raw.bam.sort |2013-10-23 01:20:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.rmdup.bam |2013-10-23 01:20:36| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.header |2013-10-23 01:20:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.header |2013-10-23 01:20:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam |2013-10-23 01:20:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam |2013-10-23 01:20:42| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam.tmp.4874.smaltmap.* |2013-10-23 01:21:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.perfect |2013-10-23 01:31:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.45.reapr |2013-10-23 01:33:56| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.prob |2013-10-23 01:35:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.bam |2013-10-23 01:37:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.sorted |2013-10-23 01:37:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.sorted.bam |2013-10-23 01:37:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.55 |2013-10-23 01:38:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0 |2013-10-23 01:40:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig 100 32 |2013-10-23 01:41:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.cgal |2013-10-23 01:44:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig mira.55.ale |2013-10-23 01:56:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig |2013-10-23 01:56:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr |2013-10-23 01:56:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.cmds |2013-10-23 01:56:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.fa |2013-10-23 01:56:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 01:58:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.raw.bam |2013-10-23 02:00:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.raw.bam.sort |2013-10-23 02:01:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.rmdup.bam |2013-10-23 02:01:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.header |2013-10-23 02:01:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.header |2013-10-23 02:01:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam |2013-10-23 02:01:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam |2013-10-23 02:01:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam.tmp.8299.smaltmap.* |2013-10-23 02:01:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.perfect |2013-10-23 02:12:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.55.reapr |2013-10-23 02:16:45| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.prob |2013-10-23 02:18:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.bam |2013-10-23 02:19:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.sorted |2013-10-23 02:19:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.sorted.bam |2013-10-23 02:20:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.65 |2013-10-23 02:20:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0 |2013-10-23 02:23:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig 100 32 |2013-10-23 02:24:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.cgal |2013-10-23 02:27:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig mira.65.ale |2013-10-23 02:39:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig |2013-10-23 02:39:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr |2013-10-23 02:39:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.cmds |2013-10-23 02:39:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.fa |2013-10-23 02:39:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 02:41:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.raw.bam |2013-10-23 02:43:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.raw.bam.sort |2013-10-23 02:44:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.rmdup.bam |2013-10-23 02:44:03| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.header |2013-10-23 02:44:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.header |2013-10-23 02:44:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam |2013-10-23 02:44:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam |2013-10-23 02:44:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam.tmp.12133.smaltmap.* |2013-10-23 02:44:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.perfect |2013-10-23 02:54:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.65.reapr |2013-10-23 02:57:27| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.prob |2013-10-23 02:59:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.bam |2013-10-23 03:01:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.sorted |2013-10-23 03:01:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.sorted.bam |2013-10-23 03:01:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.75 |2013-10-23 03:02:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0 |2013-10-23 03:04:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig 100 32 |2013-10-23 03:05:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.cgal |2013-10-23 03:09:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig mira.75.ale |2013-10-23 03:20:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig |2013-10-23 03:20:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr |2013-10-23 03:20:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.cmds |2013-10-23 03:20:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.fa |2013-10-23 03:21:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 03:22:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.raw.bam |2013-10-23 03:24:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.raw.bam.sort |2013-10-23 03:25:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.rmdup.bam |2013-10-23 03:25:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.header |2013-10-23 03:25:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.header |2013-10-23 03:25:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam |2013-10-23 03:25:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam |2013-10-23 03:25:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam.tmp.15559.smaltmap.* |2013-10-23 03:25:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.perfect |2013-10-23 03:36:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.75.reapr |2013-10-23 03:38:18| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.prob |2013-10-23 03:39:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.bam |2013-10-23 03:41:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.sorted |2013-10-23 03:41:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.sorted.bam |2013-10-23 03:41:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.85 |2013-10-23 03:42:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0 |2013-10-23 03:44:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig 100 32 |2013-10-23 03:45:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.cgal |2013-10-23 03:49:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig mira.85.ale |2013-10-23 04:00:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig |2013-10-23 04:00:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr |2013-10-23 04:00:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.cmds |2013-10-23 04:00:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.fa |2013-10-23 04:00:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 04:02:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.raw.bam |2013-10-23 04:03:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.raw.bam.sort |2013-10-23 04:04:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.rmdup.bam |2013-10-23 04:04:55| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.header |2013-10-23 04:04:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.header |2013-10-23 04:04:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam |2013-10-23 04:05:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam |2013-10-23 04:05:02| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam.tmp.18875.smaltmap.* |2013-10-23 04:05:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.perfect |2013-10-23 04:15:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.85.reapr |2013-10-23 04:17:20| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file mira.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.prob |2013-10-23 04:18:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.bam |2013-10-23 04:20:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.sorted |2013-10-23 04:20:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.sorted.bam |2013-10-23 04:20:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_mira.95 |2013-10-23 04:21:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0 |2013-10-23 04:23:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig 100 32 |2013-10-23 04:24:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.cgal |2013-10-23 04:28:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig mira.95.ale |2013-10-23 04:39:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig |2013-10-23 04:39:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr |2013-10-23 04:39:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.cmds |2013-10-23 04:39:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.fa |2013-10-23 04:39:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 04:41:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.raw.bam |2013-10-23 04:42:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.raw.bam.sort |2013-10-23 04:43:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.rmdup.bam |2013-10-23 04:43:39| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.header |2013-10-23 04:43:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.header |2013-10-23 04:43:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam |2013-10-23 04:43:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam |2013-10-23 04:43:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam.tmp.22351.smaltmap.* |2013-10-23 04:44:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.perfect |2013-10-23 04:53:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/mira.95.reapr |2013-10-23 04:55:26| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.prob |2013-10-23 04:56:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.bam |2013-10-23 04:58:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.sorted |2013-10-23 04:58:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.sorted.bam |2013-10-23 04:58:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.105 |2013-10-23 04:59:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0 |2013-10-23 05:01:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig 100 32 |2013-10-23 05:02:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.cgal |2013-10-23 05:05:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig ray.105.ale |2013-10-23 05:15:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig |2013-10-23 05:15:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr |2013-10-23 05:15:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.cmds |2013-10-23 05:15:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.fa |2013-10-23 05:15:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 05:17:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.raw.bam |2013-10-23 05:18:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.raw.bam.sort |2013-10-23 05:19:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.rmdup.bam |2013-10-23 05:19:57| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.header |2013-10-23 05:19:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.header |2013-10-23 05:19:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam |2013-10-23 05:20:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam |2013-10-23 05:20:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam.tmp.25518.smaltmap.* |2013-10-23 05:20:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.perfect |2013-10-23 05:27:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.105.reapr |2013-10-23 05:29:21| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.prob |2013-10-23 05:30:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.bam |2013-10-23 05:32:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.sorted |2013-10-23 05:32:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.sorted.bam |2013-10-23 05:32:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.125 |2013-10-23 05:32:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0 |2013-10-23 05:33:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig 100 32 |2013-10-23 05:34:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.cgal |2013-10-23 05:36:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig ray.125.ale |2013-10-23 05:41:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig |2013-10-23 05:41:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr |2013-10-23 05:41:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.cmds |2013-10-23 05:41:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.fa |2013-10-23 05:41:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 05:43:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.raw.bam |2013-10-23 05:45:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.raw.bam.sort |2013-10-23 05:46:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.rmdup.bam |2013-10-23 05:46:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.header |2013-10-23 05:46:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.header |2013-10-23 05:46:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam |2013-10-23 05:46:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam |2013-10-23 05:46:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam.tmp.28243.smaltmap.* |2013-10-23 05:46:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.perfect |2013-10-23 05:49:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.125.reapr |2013-10-23 05:56:16| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.prob |2013-10-23 05:57:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.bam |2013-10-23 05:59:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.sorted |2013-10-23 05:59:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.sorted.bam |2013-10-23 05:59:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.25 |2013-10-23 06:00:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0 |2013-10-23 06:21:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig 100 32 |2013-10-23 06:23:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.cgal |2013-10-23 06:28:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig ray.25.ale |2013-10-23 06:40:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig |2013-10-23 06:40:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr |2013-10-23 06:40:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.cmds |2013-10-23 06:41:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.fa |2013-10-23 06:41:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 06:44:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.raw.bam |2013-10-23 06:46:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.raw.bam.sort |2013-10-23 06:47:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.rmdup.bam |2013-10-23 06:47:14| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.header |2013-10-23 06:47:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.header |2013-10-23 06:47:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam |2013-10-23 06:47:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam |2013-10-23 06:47:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam.tmp.2010.smaltmap.* |2013-10-23 06:49:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.perfect |2013-10-23 15:15:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.25.reapr |2013-10-23 15:19:25| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.prob |2013-10-23 15:20:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.bam |2013-10-23 15:22:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.sorted |2013-10-23 15:22:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.sorted.bam |2013-10-23 15:23:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.35 |2013-10-23 15:23:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0 |2013-10-23 15:28:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig 100 32 |2013-10-23 15:29:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.cgal |2013-10-23 15:33:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig ray.35.ale |2013-10-23 15:45:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig |2013-10-23 15:45:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr |2013-10-23 15:45:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.cmds |2013-10-23 15:46:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.fa |2013-10-23 15:46:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 15:50:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.raw.bam |2013-10-23 15:51:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.raw.bam.sort |2013-10-23 15:52:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.rmdup.bam |2013-10-23 15:52:33| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.header |2013-10-23 15:52:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.header |2013-10-23 15:52:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam |2013-10-23 15:52:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam |2013-10-23 15:52:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam.tmp.14246.smaltmap.* |2013-10-23 15:53:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.perfect |2013-10-23 16:44:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.35.reapr |2013-10-23 16:48:04| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.prob |2013-10-23 16:49:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.bam |2013-10-23 16:51:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.sorted |2013-10-23 16:52:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.sorted.bam |2013-10-23 16:52:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.41 |2013-10-23 16:53:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0 |2013-10-23 16:55:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig 100 32 |2013-10-23 16:57:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.cgal |2013-10-23 17:00:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig ray.41.ale |2013-10-23 17:12:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig |2013-10-23 17:12:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr |2013-10-23 17:12:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.cmds |2013-10-23 17:12:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.fa |2013-10-23 17:13:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 17:19:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.raw.bam |2013-10-23 17:21:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.raw.bam.sort |2013-10-23 17:22:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.rmdup.bam |2013-10-23 17:22:04| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.header |2013-10-23 17:22:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.header |2013-10-23 17:22:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam |2013-10-23 17:22:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam |2013-10-23 17:22:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam.tmp.23508.smaltmap.* |2013-10-23 17:22:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.perfect |2013-10-23 17:37:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.41.reapr |2013-10-23 17:39:49| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.prob |2013-10-23 17:41:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.bam |2013-10-23 17:42:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.sorted |2013-10-23 17:43:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.sorted.bam |2013-10-23 17:43:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.45 |2013-10-23 17:43:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0 |2013-10-23 17:46:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig 100 32 |2013-10-23 17:47:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.cgal |2013-10-23 17:51:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig ray.45.ale |2013-10-23 18:03:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig |2013-10-23 18:03:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr |2013-10-23 18:03:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.cmds |2013-10-23 18:03:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.fa |2013-10-23 18:04:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 18:11:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.raw.bam |2013-10-23 18:12:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.raw.bam.sort |2013-10-23 18:13:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.rmdup.bam |2013-10-23 18:13:42| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.header |2013-10-23 18:13:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.header |2013-10-23 18:13:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam |2013-10-23 18:13:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam |2013-10-23 18:13:49| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam.tmp.28720.smaltmap.* |2013-10-23 18:14:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.perfect |2013-10-23 18:25:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.45.reapr |2013-10-23 18:30:01| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.prob |2013-10-23 18:31:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.bam |2013-10-23 18:33:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.sorted |2013-10-23 18:33:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.sorted.bam |2013-10-23 18:33:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.55 |2013-10-23 18:34:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0 |2013-10-23 18:37:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig 100 32 |2013-10-23 18:38:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.cgal |2013-10-23 18:42:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig ray.55.ale |2013-10-23 18:56:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig |2013-10-23 18:56:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr |2013-10-23 18:56:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.cmds |2013-10-23 18:56:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.fa |2013-10-23 18:56:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 19:00:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.raw.bam |2013-10-23 19:02:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.raw.bam.sort |2013-10-23 19:03:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.rmdup.bam |2013-10-23 19:03:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.header |2013-10-23 19:03:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.header |2013-10-23 19:03:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam |2013-10-23 19:03:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam |2013-10-23 19:03:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam.tmp.1532.smaltmap.* |2013-10-23 19:03:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.perfect |2013-10-23 19:15:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.55.reapr |2013-10-23 19:19:21| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.prob |2013-10-23 19:20:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.bam |2013-10-23 19:22:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.sorted |2013-10-23 19:22:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.sorted.bam |2013-10-23 19:23:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.65 |2013-10-23 19:23:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0 |2013-10-23 19:26:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig 100 32 |2013-10-23 19:27:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.cgal |2013-10-23 19:31:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig ray.65.ale |2013-10-23 19:43:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig |2013-10-23 19:43:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr |2013-10-23 19:43:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.cmds |2013-10-23 19:43:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.fa |2013-10-23 19:44:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 19:47:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.raw.bam |2013-10-23 19:48:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.raw.bam.sort |2013-10-23 19:49:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.rmdup.bam |2013-10-23 19:49:49| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.header |2013-10-23 19:49:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.header |2013-10-23 19:49:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam |2013-10-23 19:49:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam |2013-10-23 19:49:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam.tmp.6014.smaltmap.* |2013-10-23 19:50:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.perfect |2013-10-23 20:00:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.65.reapr |2013-10-23 20:04:24| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.prob |2013-10-23 20:05:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.bam |2013-10-23 20:07:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.sorted |2013-10-23 20:07:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.sorted.bam |2013-10-23 20:08:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.75 |2013-10-23 20:08:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0 |2013-10-23 20:11:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig 100 32 |2013-10-23 20:12:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.cgal |2013-10-23 20:15:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig ray.75.ale |2013-10-23 20:28:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig |2013-10-23 20:28:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr |2013-10-23 20:28:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.cmds |2013-10-23 20:28:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.fa |2013-10-23 20:28:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 20:33:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.raw.bam |2013-10-23 20:35:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.raw.bam.sort |2013-10-23 20:36:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.rmdup.bam |2013-10-23 20:36:23| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.header |2013-10-23 20:36:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.header |2013-10-23 20:36:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam |2013-10-23 20:36:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam |2013-10-23 20:36:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam.tmp.9975.smaltmap.* |2013-10-23 20:37:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.perfect |2013-10-23 20:46:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.75.reapr |2013-10-23 20:50:17| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.prob |2013-10-23 20:51:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.bam |2013-10-23 20:53:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.sorted |2013-10-23 20:53:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.sorted.bam |2013-10-23 20:54:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.85 |2013-10-23 20:54:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0 |2013-10-23 20:57:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig 100 32 |2013-10-23 20:58:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.cgal |2013-10-23 21:01:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig ray.85.ale |2013-10-23 21:13:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig |2013-10-23 21:13:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr |2013-10-23 21:13:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.cmds |2013-10-23 21:13:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.fa |2013-10-23 21:13:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 21:16:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.raw.bam |2013-10-23 21:17:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.raw.bam.sort |2013-10-23 21:18:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.rmdup.bam |2013-10-23 21:18:55| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.header |2013-10-23 21:18:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.header |2013-10-23 21:18:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam |2013-10-23 21:19:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam |2013-10-23 21:19:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam.tmp.13908.smaltmap.* |2013-10-23 21:19:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.perfect |2013-10-23 21:28:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.85.reapr |2013-10-23 21:31:58| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file ray.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.prob |2013-10-23 21:33:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.bam |2013-10-23 21:34:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.sorted |2013-10-23 21:35:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.sorted.bam |2013-10-23 21:35:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_ray.95 |2013-10-23 21:35:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0 |2013-10-23 21:38:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig 100 32 |2013-10-23 21:39:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.cgal |2013-10-23 21:42:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig ray.95.ale |2013-10-23 21:52:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig |2013-10-23 21:52:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr |2013-10-23 21:52:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.cmds |2013-10-23 21:52:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.fa |2013-10-23 21:53:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 21:55:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.raw.bam |2013-10-23 21:56:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.raw.bam.sort |2013-10-23 21:57:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.rmdup.bam |2013-10-23 21:57:33| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.header |2013-10-23 21:57:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.header |2013-10-23 21:57:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam |2013-10-23 21:57:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam |2013-10-23 21:57:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam.tmp.17342.smaltmap.* |2013-10-23 21:58:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.perfect |2013-10-23 22:06:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/ray.95.reapr |2013-10-23 22:07:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.prob |2013-10-23 22:09:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.bam |2013-10-23 22:10:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.sorted |2013-10-23 22:10:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.sorted.bam |2013-10-23 22:11:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.105 |2013-10-23 22:11:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0 |2013-10-23 22:13:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig 100 32 |2013-10-23 22:14:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.cgal |2013-10-23 22:17:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig sga.105.ale |2013-10-23 22:26:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig |2013-10-23 22:26:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr |2013-10-23 22:26:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.cmds |2013-10-23 22:26:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.fa |2013-10-23 22:26:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 22:28:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.raw.bam |2013-10-23 22:30:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.raw.bam.sort |2013-10-23 22:31:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.rmdup.bam |2013-10-23 22:31:20| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.header |2013-10-23 22:31:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.header |2013-10-23 22:31:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam |2013-10-23 22:31:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam |2013-10-23 22:31:26| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam.tmp.20415.smaltmap.* |2013-10-23 22:31:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.perfect |2013-10-23 22:38:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.105.reapr |2013-10-23 22:40:34| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.prob |2013-10-23 22:41:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.bam |2013-10-23 22:43:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.sorted |2013-10-23 22:43:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.sorted.bam |2013-10-23 22:44:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.125 |2013-10-23 22:44:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0 |2013-10-23 22:46:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig 100 32 |2013-10-23 22:47:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.cgal |2013-10-23 22:50:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig sga.125.ale |2013-10-23 22:58:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig |2013-10-23 22:58:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr |2013-10-23 22:58:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.cmds |2013-10-23 22:58:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.fa |2013-10-23 22:58:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 23:00:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.raw.bam |2013-10-23 23:02:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.raw.bam.sort |2013-10-23 23:03:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.rmdup.bam |2013-10-23 23:03:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.header |2013-10-23 23:03:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.header |2013-10-23 23:03:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam |2013-10-23 23:03:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam |2013-10-23 23:03:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam.tmp.24618.smaltmap.* |2013-10-23 23:03:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.perfect |2013-10-23 23:11:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.125.reapr |2013-10-23 23:13:56| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.prob |2013-10-23 23:15:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.bam |2013-10-23 23:16:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.sorted |2013-10-23 23:16:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.sorted.bam |2013-10-23 23:17:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.25 |2013-10-23 23:17:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0 |2013-10-23 23:20:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig 100 32 |2013-10-23 23:21:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.cgal |2013-10-23 23:24:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig sga.25.ale |2013-10-23 23:33:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig |2013-10-23 23:33:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr |2013-10-23 23:33:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.cmds |2013-10-23 23:33:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.fa |2013-10-23 23:33:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-23 23:36:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.raw.bam |2013-10-23 23:38:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.raw.bam.sort |2013-10-23 23:39:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.rmdup.bam |2013-10-23 23:39:14| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.header |2013-10-23 23:39:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.header |2013-10-23 23:39:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam |2013-10-23 23:39:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam |2013-10-23 23:39:21| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam.tmp.29312.smaltmap.* |2013-10-23 23:39:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.perfect |2013-10-23 23:49:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.25.reapr |2013-10-23 23:52:20| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.prob |2013-10-23 23:53:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.bam |2013-10-23 23:55:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.sorted |2013-10-23 23:55:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.sorted.bam |2013-10-23 23:55:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.35 |2013-10-23 23:56:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0 |2013-10-23 23:58:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig 100 32 |2013-10-23 23:59:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.cgal |2013-10-24 00:02:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig sga.35.ale |2013-10-24 00:11:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig |2013-10-24 00:11:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr |2013-10-24 00:11:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.cmds |2013-10-24 00:11:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.fa |2013-10-24 00:12:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 00:15:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.raw.bam |2013-10-24 00:16:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.raw.bam.sort |2013-10-24 00:17:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.rmdup.bam |2013-10-24 00:17:25| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.header |2013-10-24 00:17:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.header |2013-10-24 00:17:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam |2013-10-24 00:17:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam |2013-10-24 00:17:32| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam.tmp.939.smaltmap.* |2013-10-24 00:18:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.perfect |2013-10-24 00:27:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.35.reapr |2013-10-24 00:29:33| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.prob |2013-10-24 00:30:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.bam |2013-10-24 00:32:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.sorted |2013-10-24 00:32:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.sorted.bam |2013-10-24 00:32:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.41 |2013-10-24 00:33:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0 |2013-10-24 00:35:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig 100 32 |2013-10-24 00:36:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.cgal |2013-10-24 00:39:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig sga.41.ale |2013-10-24 00:49:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig |2013-10-24 00:49:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr |2013-10-24 00:49:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.cmds |2013-10-24 00:49:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.fa |2013-10-24 00:49:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 00:52:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.raw.bam |2013-10-24 00:53:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.raw.bam.sort |2013-10-24 00:54:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.rmdup.bam |2013-10-24 00:54:26| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.header |2013-10-24 00:54:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.header |2013-10-24 00:54:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam |2013-10-24 00:54:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam |2013-10-24 00:54:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam.tmp.5196.smaltmap.* |2013-10-24 00:55:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.perfect |2013-10-24 01:03:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.41.reapr |2013-10-24 01:06:36| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.prob |2013-10-24 01:07:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.bam |2013-10-24 01:09:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.sorted |2013-10-24 01:09:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.sorted.bam |2013-10-24 01:10:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.45 |2013-10-24 01:10:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0 |2013-10-24 01:12:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig 100 32 |2013-10-24 01:13:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.cgal |2013-10-24 01:16:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig sga.45.ale |2013-10-24 01:25:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig |2013-10-24 01:25:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr |2013-10-24 01:25:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.cmds |2013-10-24 01:26:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.fa |2013-10-24 01:26:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 01:28:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.raw.bam |2013-10-24 01:30:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.raw.bam.sort |2013-10-24 01:31:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.rmdup.bam |2013-10-24 01:31:14| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.header |2013-10-24 01:31:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.header |2013-10-24 01:31:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam |2013-10-24 01:31:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam |2013-10-24 01:31:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam.tmp.9318.smaltmap.* |2013-10-24 01:31:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.perfect |2013-10-24 01:40:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.45.reapr |2013-10-24 01:42:47| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.prob |2013-10-24 01:44:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.bam |2013-10-24 01:45:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.sorted |2013-10-24 01:45:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.sorted.bam |2013-10-24 01:46:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.55 |2013-10-24 01:46:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0 |2013-10-24 01:48:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig 100 32 |2013-10-24 01:49:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.cgal |2013-10-24 01:52:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig sga.55.ale |2013-10-24 02:01:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig |2013-10-24 02:01:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr |2013-10-24 02:01:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.cmds |2013-10-24 02:02:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.fa |2013-10-24 02:02:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 02:04:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.raw.bam |2013-10-24 02:06:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.raw.bam.sort |2013-10-24 02:07:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.rmdup.bam |2013-10-24 02:07:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.header |2013-10-24 02:07:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.header |2013-10-24 02:07:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam |2013-10-24 02:07:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam |2013-10-24 02:07:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam.tmp.13590.smaltmap.* |2013-10-24 02:07:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.perfect |2013-10-24 02:16:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.55.reapr |2013-10-24 02:18:11| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.prob |2013-10-24 02:19:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.bam |2013-10-24 02:21:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.sorted |2013-10-24 02:21:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.sorted.bam |2013-10-24 02:21:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.65 |2013-10-24 02:22:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0 |2013-10-24 02:24:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig 100 32 |2013-10-24 02:25:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.cgal |2013-10-24 02:27:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig sga.65.ale |2013-10-24 02:37:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig |2013-10-24 02:37:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr |2013-10-24 02:37:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.cmds |2013-10-24 02:37:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.fa |2013-10-24 02:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 02:39:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.raw.bam |2013-10-24 02:41:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.raw.bam.sort |2013-10-24 02:42:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.rmdup.bam |2013-10-24 02:42:15| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.header |2013-10-24 02:42:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.header |2013-10-24 02:42:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam |2013-10-24 02:42:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam |2013-10-24 02:42:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam.tmp.17618.smaltmap.* |2013-10-24 02:42:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.perfect |2013-10-24 02:50:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.65.reapr |2013-10-24 02:53:01| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.prob |2013-10-24 02:54:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.bam |2013-10-24 02:55:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.sorted |2013-10-24 02:56:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.sorted.bam |2013-10-24 02:56:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.75 |2013-10-24 02:56:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0 |2013-10-24 02:58:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig 100 32 |2013-10-24 02:59:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.cgal |2013-10-24 03:02:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig sga.75.ale |2013-10-24 03:11:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig |2013-10-24 03:11:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr |2013-10-24 03:11:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.cmds |2013-10-24 03:11:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.fa |2013-10-24 03:12:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 03:14:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.raw.bam |2013-10-24 03:15:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.raw.bam.sort |2013-10-24 03:16:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.rmdup.bam |2013-10-24 03:16:58| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.header |2013-10-24 03:16:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.header |2013-10-24 03:16:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam |2013-10-24 03:17:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam |2013-10-24 03:17:04| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam.tmp.21706.smaltmap.* |2013-10-24 03:17:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.perfect |2013-10-24 03:25:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.75.reapr |2013-10-24 03:27:18| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.prob |2013-10-24 03:28:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.bam |2013-10-24 03:30:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.sorted |2013-10-24 03:30:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.sorted.bam |2013-10-24 03:30:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.85 |2013-10-24 03:31:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0 |2013-10-24 03:33:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig 100 32 |2013-10-24 03:34:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.cgal |2013-10-24 03:36:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig sga.85.ale |2013-10-24 03:45:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig |2013-10-24 03:45:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr |2013-10-24 03:45:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.cmds |2013-10-24 03:45:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.fa |2013-10-24 03:46:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 03:48:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.raw.bam |2013-10-24 03:49:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.raw.bam.sort |2013-10-24 03:50:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.rmdup.bam |2013-10-24 03:50:58| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.header |2013-10-24 03:50:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.header |2013-10-24 03:51:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam |2013-10-24 03:51:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam |2013-10-24 03:51:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam.tmp.25834.smaltmap.* |2013-10-24 03:51:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.perfect |2013-10-24 03:59:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.85.reapr |2013-10-24 04:01:12| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sga.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.prob |2013-10-24 04:02:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.bam |2013-10-24 04:04:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.sorted |2013-10-24 04:04:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.sorted.bam |2013-10-24 04:04:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sga.95 |2013-10-24 04:05:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0 |2013-10-24 04:06:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig 100 32 |2013-10-24 04:07:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.cgal |2013-10-24 04:10:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig sga.95.ale |2013-10-24 04:19:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig |2013-10-24 04:19:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr |2013-10-24 04:19:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.cmds |2013-10-24 04:19:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.fa |2013-10-24 04:19:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 04:22:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.raw.bam |2013-10-24 04:23:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.raw.bam.sort |2013-10-24 04:24:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.rmdup.bam |2013-10-24 04:24:40| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.header |2013-10-24 04:24:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.header |2013-10-24 04:24:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam |2013-10-24 04:24:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam |2013-10-24 04:24:47| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam.tmp.30087.smaltmap.* |2013-10-24 04:25:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.perfect |2013-10-24 04:32:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sga.95.reapr |2013-10-24 04:34:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.prob |2013-10-24 04:35:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.bam |2013-10-24 04:37:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.sorted |2013-10-24 04:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.sorted.bam |2013-10-24 04:37:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.25 |2013-10-24 04:38:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0 |2013-10-24 04:43:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig 100 32 |2013-10-24 04:44:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.cgal |2013-10-24 04:48:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig soapdenovo2.25.ale |2013-10-24 04:58:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig |2013-10-24 04:58:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr |2013-10-24 04:58:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.cmds |2013-10-24 04:58:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.fa |2013-10-24 04:59:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 05:02:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.raw.bam |2013-10-24 05:04:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.raw.bam.sort |2013-10-24 05:05:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.rmdup.bam |2013-10-24 05:05:16| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.header |2013-10-24 05:05:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.header |2013-10-24 05:05:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam |2013-10-24 05:05:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam |2013-10-24 05:05:23| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam.tmp.2302.smaltmap.* |2013-10-24 05:06:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.perfect |2013-10-24 05:19:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.25.reapr |2013-10-24 05:21:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.prob |2013-10-24 05:23:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.bam |2013-10-24 05:24:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.sorted |2013-10-24 05:25:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.sorted.bam |2013-10-24 05:25:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.35 |2013-10-24 05:25:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0 |2013-10-24 05:28:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig 100 32 |2013-10-24 05:29:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.cgal |2013-10-24 05:32:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig soapdenovo2.35.ale |2013-10-24 05:44:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig |2013-10-24 05:44:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr |2013-10-24 05:44:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.cmds |2013-10-24 05:44:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.fa |2013-10-24 05:45:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 05:47:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.raw.bam |2013-10-24 05:49:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.raw.bam.sort |2013-10-24 05:50:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.rmdup.bam |2013-10-24 05:50:24| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.header |2013-10-24 05:50:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.header |2013-10-24 05:50:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam |2013-10-24 05:50:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam |2013-10-24 05:50:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam.tmp.6397.smaltmap.* |2013-10-24 05:50:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.perfect |2013-10-24 06:01:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.35.reapr |2013-10-24 06:03:43| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.prob |2013-10-24 06:05:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.bam |2013-10-24 06:06:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.sorted |2013-10-24 06:06:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.sorted.bam |2013-10-24 06:07:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.41 |2013-10-24 06:07:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0 |2013-10-24 06:09:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig 100 32 |2013-10-24 06:11:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.cgal |2013-10-24 06:14:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig soapdenovo2.41.ale |2013-10-24 06:26:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig |2013-10-24 06:26:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr |2013-10-24 06:26:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.cmds |2013-10-24 06:26:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.fa |2013-10-24 06:26:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 06:29:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.raw.bam |2013-10-24 06:30:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.raw.bam.sort |2013-10-24 06:31:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.rmdup.bam |2013-10-24 06:31:46| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.header |2013-10-24 06:31:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.header |2013-10-24 06:31:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam |2013-10-24 06:31:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam |2013-10-24 06:31:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam.tmp.9943.smaltmap.* |2013-10-24 06:32:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.perfect |2013-10-24 06:43:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.41.reapr |2013-10-24 06:45:07| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.prob |2013-10-24 06:46:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.bam |2013-10-24 06:48:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.sorted |2013-10-24 06:48:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.sorted.bam |2013-10-24 06:48:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.45 |2013-10-24 06:49:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0 |2013-10-24 06:51:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig 100 32 |2013-10-24 06:52:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.cgal |2013-10-24 06:55:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig soapdenovo2.45.ale |2013-10-24 07:07:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig |2013-10-24 07:07:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr |2013-10-24 07:07:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.cmds |2013-10-24 07:07:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.fa |2013-10-24 07:08:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 07:10:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.raw.bam |2013-10-24 07:12:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.raw.bam.sort |2013-10-24 07:13:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.rmdup.bam |2013-10-24 07:13:10| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.header |2013-10-24 07:13:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.header |2013-10-24 07:13:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam |2013-10-24 07:13:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam |2013-10-24 07:13:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam.tmp.13609.smaltmap.* |2013-10-24 07:13:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.perfect |2013-10-24 07:24:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.45.reapr |2013-10-24 07:26:34| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.prob |2013-10-24 07:27:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.bam |2013-10-24 07:29:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.sorted |2013-10-24 07:29:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.sorted.bam |2013-10-24 07:30:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.55 |2013-10-24 07:30:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0 |2013-10-24 07:32:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig 100 32 |2013-10-24 07:34:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.cgal |2013-10-24 07:37:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig soapdenovo2.55.ale |2013-10-24 07:49:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig |2013-10-24 07:49:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr |2013-10-24 07:49:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.cmds |2013-10-24 07:49:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.fa |2013-10-24 07:49:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 07:52:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.raw.bam |2013-10-24 07:54:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.raw.bam.sort |2013-10-24 07:55:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.rmdup.bam |2013-10-24 07:55:23| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.header |2013-10-24 07:55:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.header |2013-10-24 07:55:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam |2013-10-24 07:55:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam |2013-10-24 07:55:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam.tmp.17026.smaltmap.* |2013-10-24 07:55:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.perfect |2013-10-24 08:06:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.55.reapr |2013-10-24 08:08:41| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.prob |2013-10-24 08:10:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.bam |2013-10-24 08:11:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.sorted |2013-10-24 08:11:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.sorted.bam |2013-10-24 08:12:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.65 |2013-10-24 08:12:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0 |2013-10-24 08:14:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig 100 32 |2013-10-24 08:16:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.cgal |2013-10-24 08:19:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig soapdenovo2.65.ale |2013-10-24 08:31:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig |2013-10-24 08:31:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr |2013-10-24 08:31:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.cmds |2013-10-24 08:31:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.fa |2013-10-24 08:31:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 08:34:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.raw.bam |2013-10-24 08:35:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.raw.bam.sort |2013-10-24 08:36:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.rmdup.bam |2013-10-24 08:36:59| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.header |2013-10-24 08:36:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.header |2013-10-24 08:37:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam |2013-10-24 08:37:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam |2013-10-24 08:37:05| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam.tmp.20523.smaltmap.* |2013-10-24 08:37:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.perfect |2013-10-24 08:48:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.65.reapr |2013-10-24 08:50:21| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.prob |2013-10-24 08:51:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.bam |2013-10-24 08:53:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.sorted |2013-10-24 08:53:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.sorted.bam |2013-10-24 08:53:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.75 |2013-10-24 08:54:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0 |2013-10-24 08:56:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig 100 32 |2013-10-24 08:57:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.cgal |2013-10-24 09:01:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig soapdenovo2.75.ale |2013-10-24 09:13:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig |2013-10-24 09:13:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr |2013-10-24 09:13:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.cmds |2013-10-24 09:13:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.fa |2013-10-24 09:13:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 09:16:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.raw.bam |2013-10-24 09:17:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.raw.bam.sort |2013-10-24 09:18:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.rmdup.bam |2013-10-24 09:18:31| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.header |2013-10-24 09:18:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.header |2013-10-24 09:18:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam |2013-10-24 09:18:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam |2013-10-24 09:18:38| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam.tmp.24088.smaltmap.* |2013-10-24 09:19:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.perfect |2013-10-24 09:29:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.75.reapr |2013-10-24 09:31:17| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.prob |2013-10-24 09:32:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.bam |2013-10-24 09:34:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.sorted |2013-10-24 09:34:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.sorted.bam |2013-10-24 09:34:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.85 |2013-10-24 09:35:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0 |2013-10-24 09:36:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig 100 32 |2013-10-24 09:37:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.cgal |2013-10-24 09:40:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig soapdenovo2.85.ale |2013-10-24 09:49:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig |2013-10-24 09:49:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr |2013-10-24 09:49:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.cmds |2013-10-24 09:49:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.fa |2013-10-24 09:50:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 09:52:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.raw.bam |2013-10-24 09:53:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.raw.bam.sort |2013-10-24 09:54:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.rmdup.bam |2013-10-24 09:54:37| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.header |2013-10-24 09:54:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.header |2013-10-24 09:54:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam |2013-10-24 09:54:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam |2013-10-24 09:54:43| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam.tmp.27273.smaltmap.* |2013-10-24 09:55:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.perfect |2013-10-24 10:02:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.85.reapr |2013-10-24 10:03:12| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file soapdenovo2.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.prob |2013-10-24 10:04:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.bam |2013-10-24 10:05:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.sorted |2013-10-24 10:05:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.sorted.bam |2013-10-24 10:06:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_soapdenovo2.95 |2013-10-24 10:06:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0 |2013-10-24 10:06:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig 100 32 |2013-10-24 10:06:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.cgal |2013-10-24 10:07:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig soapdenovo2.95.ale |2013-10-24 10:08:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig |2013-10-24 10:08:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr |2013-10-24 10:08:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.cmds |2013-10-24 10:08:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.fa |2013-10-24 10:09:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 10:10:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.raw.bam |2013-10-24 10:11:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.raw.bam.sort |2013-10-24 10:12:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.rmdup.bam |2013-10-24 10:12:25| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.header |2013-10-24 10:12:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.header |2013-10-24 10:12:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam |2013-10-24 10:12:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam |2013-10-24 10:12:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam.tmp.29965.smaltmap.* |2013-10-24 10:12:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.perfect |2013-10-24 10:13:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/soapdenovo2.95.reapr |2013-10-24 10:15:07| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.prob |2013-10-24 10:16:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.bam |2013-10-24 10:18:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.sorted |2013-10-24 10:18:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.sorted.bam |2013-10-24 10:18:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.105 |2013-10-24 10:19:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0 |2013-10-24 10:21:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig 100 32 |2013-10-24 10:22:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.cgal |2013-10-24 10:26:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig spades.105.ale |2013-10-24 10:38:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig |2013-10-24 10:38:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr |2013-10-24 10:38:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.cmds |2013-10-24 10:38:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.fa |2013-10-24 10:38:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 10:40:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.raw.bam |2013-10-24 10:41:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.raw.bam.sort |2013-10-24 10:42:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.rmdup.bam |2013-10-24 10:42:55| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.header |2013-10-24 10:42:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.header |2013-10-24 10:42:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam |2013-10-24 10:43:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam |2013-10-24 10:43:03| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam.tmp.32443.smaltmap.* |2013-10-24 10:43:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.perfect |2013-10-24 10:55:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.105.reapr |2013-10-24 10:57:53| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.prob |2013-10-24 11:00:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.bam |2013-10-24 11:02:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.sorted |2013-10-24 11:02:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.sorted.bam |2013-10-24 11:02:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.125 |2013-10-24 11:03:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0 |2013-10-24 11:05:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig 100 32 |2013-10-24 11:06:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.cgal |2013-10-24 11:10:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig spades.125.ale |2013-10-24 11:22:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig |2013-10-24 11:22:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr |2013-10-24 11:22:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.cmds |2013-10-24 11:22:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.fa |2013-10-24 11:22:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 11:24:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.raw.bam |2013-10-24 11:26:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.raw.bam.sort |2013-10-24 11:27:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.rmdup.bam |2013-10-24 11:27:43| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.header |2013-10-24 11:27:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.header |2013-10-24 11:27:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam |2013-10-24 11:27:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam |2013-10-24 11:27:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam.tmp.7192.smaltmap.* |2013-10-24 11:28:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.perfect |2013-10-24 11:41:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.125.reapr |2013-10-24 11:43:32| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.prob |2013-10-24 11:46:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.bam |2013-10-24 11:47:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.sorted |2013-10-24 11:47:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.sorted.bam |2013-10-24 11:48:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.25 |2013-10-24 11:48:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0 |2013-10-24 11:51:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig 100 32 |2013-10-24 11:52:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.cgal |2013-10-24 11:55:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig spades.25.ale |2013-10-24 12:07:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig |2013-10-24 12:07:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr |2013-10-24 12:07:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.cmds |2013-10-24 12:08:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.fa |2013-10-24 12:08:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 12:10:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.raw.bam |2013-10-24 12:12:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.raw.bam.sort |2013-10-24 12:13:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.rmdup.bam |2013-10-24 12:13:13| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.header |2013-10-24 12:13:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.header |2013-10-24 12:13:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam |2013-10-24 12:13:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam |2013-10-24 12:13:20| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam.tmp.15091.smaltmap.* |2013-10-24 12:13:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.perfect |2013-10-24 12:27:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.25.reapr |2013-10-24 12:30:41| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.prob |2013-10-24 12:32:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.bam |2013-10-24 12:33:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.sorted |2013-10-24 12:33:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.sorted.bam |2013-10-24 12:34:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.35 |2013-10-24 12:34:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0 |2013-10-24 12:37:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig 100 32 |2013-10-24 12:38:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.cgal |2013-10-24 12:41:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig spades.35.ale |2013-10-24 12:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig |2013-10-24 12:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr |2013-10-24 12:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.cmds |2013-10-24 12:53:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.fa |2013-10-24 12:54:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 12:56:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.raw.bam |2013-10-24 12:58:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.raw.bam.sort |2013-10-24 12:59:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.rmdup.bam |2013-10-24 12:59:05| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.header |2013-10-24 12:59:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.header |2013-10-24 12:59:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam |2013-10-24 12:59:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam |2013-10-24 12:59:11| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam.tmp.26076.smaltmap.* |2013-10-24 12:59:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.perfect |2013-10-24 13:11:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.35.reapr |2013-10-24 13:13:43| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.prob |2013-10-24 13:15:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.bam |2013-10-24 13:16:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.sorted |2013-10-24 13:16:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.sorted.bam |2013-10-24 13:17:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.41 |2013-10-24 13:17:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0 |2013-10-24 13:19:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig 100 32 |2013-10-24 13:21:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.cgal |2013-10-24 13:24:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig spades.41.ale |2013-10-24 13:36:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig |2013-10-24 13:36:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr |2013-10-24 13:36:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.cmds |2013-10-24 13:36:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.fa |2013-10-24 13:37:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 13:39:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.raw.bam |2013-10-24 13:40:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.raw.bam.sort |2013-10-24 13:41:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.rmdup.bam |2013-10-24 13:41:54| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.header |2013-10-24 13:41:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.header |2013-10-24 13:41:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam |2013-10-24 13:42:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam |2013-10-24 13:42:01| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam.tmp.29609.smaltmap.* |2013-10-24 13:42:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.perfect |2013-10-24 13:54:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.41.reapr |2013-10-24 13:56:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.prob |2013-10-24 13:58:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.bam |2013-10-24 14:00:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.sorted |2013-10-24 14:00:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.sorted.bam |2013-10-24 14:00:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.45 |2013-10-24 14:01:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0 |2013-10-24 14:03:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig 100 32 |2013-10-24 14:04:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.cgal |2013-10-24 14:07:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig spades.45.ale |2013-10-24 14:19:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig |2013-10-24 14:19:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr |2013-10-24 14:19:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.cmds |2013-10-24 14:19:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.fa |2013-10-24 14:20:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 14:22:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.raw.bam |2013-10-24 14:24:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.raw.bam.sort |2013-10-24 14:25:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.rmdup.bam |2013-10-24 14:25:07| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.header |2013-10-24 14:25:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.header |2013-10-24 14:25:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam |2013-10-24 14:25:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam |2013-10-24 14:25:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam.tmp.863.smaltmap.* |2013-10-24 14:25:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.perfect |2013-10-24 14:37:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.45.reapr |2013-10-24 14:39:55| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.prob |2013-10-24 14:41:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.bam |2013-10-24 14:42:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.sorted |2013-10-24 14:43:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.sorted.bam |2013-10-24 14:43:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.55 |2013-10-24 14:44:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0 |2013-10-24 14:46:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig 100 32 |2013-10-24 14:47:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.cgal |2013-10-24 14:50:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig spades.55.ale |2013-10-24 15:03:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig |2013-10-24 15:03:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr |2013-10-24 15:03:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.cmds |2013-10-24 15:03:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.fa |2013-10-24 15:03:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 15:05:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.raw.bam |2013-10-24 15:07:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.raw.bam.sort |2013-10-24 15:08:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.rmdup.bam |2013-10-24 15:08:01| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.header |2013-10-24 15:08:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.header |2013-10-24 15:08:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam |2013-10-24 15:08:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam |2013-10-24 15:08:07| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam.tmp.4549.smaltmap.* |2013-10-24 15:08:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.perfect |2013-10-24 15:20:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.55.reapr |2013-10-24 15:23:11| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.prob |2013-10-24 15:24:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.bam |2013-10-24 15:26:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.sorted |2013-10-24 15:26:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.sorted.bam |2013-10-24 15:26:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.65 |2013-10-24 15:27:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0 |2013-10-24 15:29:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig 100 32 |2013-10-24 15:30:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.cgal |2013-10-24 15:34:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig spades.65.ale |2013-10-24 15:46:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig |2013-10-24 15:46:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr |2013-10-24 15:46:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.cmds |2013-10-24 15:46:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.fa |2013-10-24 15:46:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 15:48:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.raw.bam |2013-10-24 15:50:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.raw.bam.sort |2013-10-24 15:51:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.rmdup.bam |2013-10-24 15:51:25| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.header |2013-10-24 15:51:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.header |2013-10-24 15:51:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam |2013-10-24 15:51:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam |2013-10-24 15:51:33| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam.tmp.8213.smaltmap.* |2013-10-24 15:52:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.perfect |2013-10-24 16:04:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.65.reapr |2013-10-24 16:09:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.prob |2013-10-24 16:11:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.bam |2013-10-24 16:13:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.sorted |2013-10-24 16:13:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.sorted.bam |2013-10-24 16:13:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.75 |2013-10-24 16:14:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0 |2013-10-24 16:16:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig 100 32 |2013-10-24 16:17:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.cgal |2013-10-24 16:21:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig spades.75.ale |2013-10-24 16:33:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig |2013-10-24 16:33:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr |2013-10-24 16:33:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.cmds |2013-10-24 16:33:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.fa |2013-10-24 16:34:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 16:36:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.raw.bam |2013-10-24 16:37:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.raw.bam.sort |2013-10-24 16:38:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.rmdup.bam |2013-10-24 16:38:50| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.header |2013-10-24 16:38:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.header |2013-10-24 16:38:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam |2013-10-24 16:38:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam |2013-10-24 16:38:57| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam.tmp.13917.smaltmap.* |2013-10-24 16:40:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.perfect |2013-10-24 16:52:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.75.reapr |2013-10-24 16:55:51| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.prob |2013-10-24 16:57:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.bam |2013-10-24 16:59:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.sorted |2013-10-24 16:59:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.sorted.bam |2013-10-24 16:59:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.85 |2013-10-24 17:00:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0 |2013-10-24 17:05:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig 100 32 |2013-10-24 17:07:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.cgal |2013-10-24 17:10:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig spades.85.ale |2013-10-24 17:22:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig |2013-10-24 17:22:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr |2013-10-24 17:22:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.cmds |2013-10-24 17:23:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.fa |2013-10-24 17:23:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 17:26:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.raw.bam |2013-10-24 17:27:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.raw.bam.sort |2013-10-24 17:28:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.rmdup.bam |2013-10-24 17:28:47| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.header |2013-10-24 17:28:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.header |2013-10-24 17:28:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam |2013-10-24 17:28:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam |2013-10-24 17:28:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam.tmp.18399.smaltmap.* |2013-10-24 17:29:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.perfect |2013-10-24 17:47:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.85.reapr |2013-10-24 17:56:48| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file spades.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.prob |2013-10-24 17:58:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.bam |2013-10-24 17:59:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.sorted |2013-10-24 18:00:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.sorted.bam |2013-10-24 18:00:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_spades.95 |2013-10-24 18:01:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0 |2013-10-24 18:03:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig 100 32 |2013-10-24 18:04:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.cgal |2013-10-24 18:09:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig spades.95.ale |2013-10-24 18:23:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig |2013-10-24 18:23:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr |2013-10-24 18:23:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.cmds |2013-10-24 18:23:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.fa |2013-10-24 18:23:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 18:25:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.raw.bam |2013-10-24 18:26:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.raw.bam.sort |2013-10-24 18:28:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.rmdup.bam |2013-10-24 18:28:23| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.header |2013-10-24 18:28:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.header |2013-10-24 18:28:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam |2013-10-24 18:28:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam |2013-10-24 18:28:31| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam.tmp.23664.smaltmap.* |2013-10-24 18:29:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.perfect |2013-10-24 18:46:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/spades.95.reapr |2013-10-24 18:51:26| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.prob |2013-10-24 18:53:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.bam |2013-10-24 18:56:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.sorted |2013-10-24 18:56:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.sorted.bam |2013-10-24 18:56:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.105 |2013-10-24 18:57:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0 |2013-10-24 18:59:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig 100 32 |2013-10-24 19:00:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.cgal |2013-10-24 19:04:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig sparseassembler.105.ale |2013-10-24 19:15:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig |2013-10-24 19:15:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr |2013-10-24 19:15:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.cmds |2013-10-24 19:15:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.fa |2013-10-24 19:16:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 19:19:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.raw.bam |2013-10-24 19:20:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.raw.bam.sort |2013-10-24 19:21:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.rmdup.bam |2013-10-24 19:21:33| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.header |2013-10-24 19:21:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.header |2013-10-24 19:21:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam |2013-10-24 19:21:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam |2013-10-24 19:21:41| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam.tmp.29212.smaltmap.* |2013-10-24 19:22:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.perfect |2013-10-24 19:31:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.105.reapr |2013-10-24 19:33:47| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.prob |2013-10-24 19:35:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.bam |2013-10-24 19:36:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.sorted |2013-10-24 19:36:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.sorted.bam |2013-10-24 19:37:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.125 |2013-10-24 19:37:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0 |2013-10-24 19:43:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig 100 32 |2013-10-24 19:44:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.cgal |2013-10-24 19:48:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig sparseassembler.125.ale |2013-10-24 20:01:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig |2013-10-24 20:01:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr |2013-10-24 20:01:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.cmds |2013-10-24 20:01:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.fa |2013-10-24 20:01:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 20:03:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.raw.bam |2013-10-24 20:05:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.raw.bam.sort |2013-10-24 20:06:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.rmdup.bam |2013-10-24 20:06:17| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.header |2013-10-24 20:06:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.header |2013-10-24 20:06:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam |2013-10-24 20:06:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam |2013-10-24 20:06:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam.tmp.6046.smaltmap.* |2013-10-24 20:06:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.perfect |2013-10-24 20:16:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.125.reapr |2013-10-24 20:21:43| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.prob |2013-10-24 20:23:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.bam |2013-10-24 20:24:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.sorted |2013-10-24 20:25:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.sorted.bam |2013-10-24 20:25:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.25 |2013-10-24 20:26:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0 |2013-10-24 20:30:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig 100 32 |2013-10-24 20:31:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.cgal |2013-10-24 20:34:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig sparseassembler.25.ale |2013-10-24 20:46:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig |2013-10-24 20:46:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr |2013-10-24 20:46:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.cmds |2013-10-24 20:46:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.fa |2013-10-24 20:46:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 20:50:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.raw.bam |2013-10-24 20:52:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.raw.bam.sort |2013-10-24 20:53:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.rmdup.bam |2013-10-24 20:53:33| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.header |2013-10-24 20:53:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.header |2013-10-24 20:53:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam |2013-10-24 20:53:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam |2013-10-24 20:53:40| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam.tmp.16469.smaltmap.* |2013-10-24 20:54:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.perfect |2013-10-24 21:03:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.25.reapr |2013-10-24 21:06:55| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.prob |2013-10-24 21:08:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.bam |2013-10-24 21:09:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.sorted |2013-10-24 21:10:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.sorted.bam |2013-10-24 21:10:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.35 |2013-10-24 21:11:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0 |2013-10-24 21:13:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig 100 32 |2013-10-24 21:14:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.cgal |2013-10-24 21:17:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig sparseassembler.35.ale |2013-10-24 21:28:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig |2013-10-24 21:28:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr |2013-10-24 21:28:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.cmds |2013-10-24 21:28:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.fa |2013-10-24 21:29:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 21:32:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.raw.bam |2013-10-24 21:33:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.raw.bam.sort |2013-10-24 21:34:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.rmdup.bam |2013-10-24 21:34:27| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.header |2013-10-24 21:34:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.header |2013-10-24 21:34:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam |2013-10-24 21:34:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam |2013-10-24 21:34:34| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam.tmp.27372.smaltmap.* |2013-10-24 21:35:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.perfect |2013-10-24 21:44:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.35.reapr |2013-10-24 21:47:55| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.prob |2013-10-24 21:49:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.bam |2013-10-24 21:50:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.sorted |2013-10-24 21:51:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.sorted.bam |2013-10-24 21:51:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.41 |2013-10-24 21:52:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0 |2013-10-24 21:54:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig 100 32 |2013-10-24 21:55:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.cgal |2013-10-24 21:58:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig sparseassembler.41.ale |2013-10-24 22:09:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig |2013-10-24 22:09:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr |2013-10-24 22:09:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.cmds |2013-10-24 22:10:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.fa |2013-10-24 22:10:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 22:13:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.raw.bam |2013-10-24 22:14:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.raw.bam.sort |2013-10-24 22:15:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.rmdup.bam |2013-10-24 22:15:31| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.header |2013-10-24 22:15:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.header |2013-10-24 22:15:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam |2013-10-24 22:15:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam |2013-10-24 22:15:39| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam.tmp.3331.smaltmap.* |2013-10-24 22:16:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.perfect |2013-10-24 22:25:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.41.reapr |2013-10-24 22:32:02| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.prob |2013-10-24 22:33:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.bam |2013-10-24 22:35:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.sorted |2013-10-24 22:35:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.sorted.bam |2013-10-24 22:35:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.45 |2013-10-24 22:36:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0 |2013-10-24 22:38:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig 100 32 |2013-10-24 22:39:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.cgal |2013-10-24 22:42:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig sparseassembler.45.ale |2013-10-24 22:54:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig |2013-10-24 22:54:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr |2013-10-24 22:54:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.cmds |2013-10-24 22:54:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.fa |2013-10-24 22:54:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 22:57:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.raw.bam |2013-10-24 22:58:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.raw.bam.sort |2013-10-24 22:59:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.rmdup.bam |2013-10-24 22:59:46| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.header |2013-10-24 22:59:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.header |2013-10-24 22:59:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam |2013-10-24 22:59:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam |2013-10-24 22:59:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam.tmp.13901.smaltmap.* |2013-10-24 23:00:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.perfect |2013-10-24 23:10:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.45.reapr |2013-10-24 23:13:49| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.prob |2013-10-24 23:15:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.bam |2013-10-24 23:16:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.sorted |2013-10-24 23:16:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.sorted.bam |2013-10-24 23:17:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.55 |2013-10-24 23:17:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0 |2013-10-24 23:20:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig 100 32 |2013-10-24 23:21:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.cgal |2013-10-24 23:24:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig sparseassembler.55.ale |2013-10-24 23:36:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig |2013-10-24 23:36:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr |2013-10-24 23:36:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.cmds |2013-10-24 23:36:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.fa |2013-10-24 23:36:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-24 23:39:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.raw.bam |2013-10-24 23:41:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.raw.bam.sort |2013-10-24 23:42:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.rmdup.bam |2013-10-24 23:42:08| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.header |2013-10-24 23:42:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.header |2013-10-24 23:42:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam |2013-10-24 23:42:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam |2013-10-24 23:42:16| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam.tmp.24196.smaltmap.* |2013-10-24 23:42:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.perfect |2013-10-24 23:52:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.55.reapr |2013-10-24 23:56:50| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.prob |2013-10-24 23:58:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.bam |2013-10-24 23:59:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.sorted |2013-10-24 23:59:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.sorted.bam |2013-10-25 00:00:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.65 |2013-10-25 00:00:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0 |2013-10-25 00:03:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig 100 32 |2013-10-25 00:04:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.cgal |2013-10-25 00:07:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig sparseassembler.65.ale |2013-10-25 00:18:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig |2013-10-25 00:18:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr |2013-10-25 00:18:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.cmds |2013-10-25 00:19:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.fa |2013-10-25 00:19:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-25 00:21:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.raw.bam |2013-10-25 00:23:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.raw.bam.sort |2013-10-25 00:24:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.rmdup.bam |2013-10-25 00:24:17| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.header |2013-10-25 00:24:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.header |2013-10-25 00:24:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam |2013-10-25 00:24:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam |2013-10-25 00:24:24| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam.tmp.343.smaltmap.* |2013-10-25 00:24:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.perfect |2013-10-25 00:34:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.65.reapr |2013-10-25 00:39:41| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.prob |2013-10-25 00:41:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.bam |2013-10-25 00:42:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.sorted |2013-10-25 00:42:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.sorted.bam |2013-10-25 00:43:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.75 |2013-10-25 00:43:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0 |2013-10-25 00:46:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig 100 32 |2013-10-25 00:47:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.cgal |2013-10-25 00:50:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig sparseassembler.75.ale |2013-10-25 01:01:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig |2013-10-25 01:01:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr |2013-10-25 01:01:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.cmds |2013-10-25 01:01:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.fa |2013-10-25 01:02:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-25 01:04:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.raw.bam |2013-10-25 01:05:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.raw.bam.sort |2013-10-25 01:06:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.rmdup.bam |2013-10-25 01:06:46| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.header |2013-10-25 01:06:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.header |2013-10-25 01:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam |2013-10-25 01:06:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam |2013-10-25 01:06:53| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam.tmp.7365.smaltmap.* |2013-10-25 01:07:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.perfect |2013-10-25 01:16:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.75.reapr |2013-10-25 01:19:42| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.prob |2013-10-25 01:21:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.bam |2013-10-25 01:22:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.sorted |2013-10-25 01:22:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.sorted.bam |2013-10-25 01:23:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.85 |2013-10-25 01:23:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0 |2013-10-25 01:26:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig 100 32 |2013-10-25 01:27:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.cgal |2013-10-25 01:30:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig sparseassembler.85.ale |2013-10-25 01:41:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig |2013-10-25 01:41:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr |2013-10-25 01:41:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.cmds |2013-10-25 01:41:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.fa |2013-10-25 01:42:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-25 01:44:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.raw.bam |2013-10-25 01:45:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.raw.bam.sort |2013-10-25 01:46:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.rmdup.bam |2013-10-25 01:46:58| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.header |2013-10-25 01:46:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.header |2013-10-25 01:46:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam |2013-10-25 01:47:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam |2013-10-25 01:47:06| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam.tmp.15941.smaltmap.* |2013-10-25 01:47:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.perfect |2013-10-25 01:56:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.85.reapr |2013-10-25 01:58:51| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file sparseassembler.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.prob |2013-10-25 02:00:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.bam |2013-10-25 02:01:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.sorted |2013-10-25 02:01:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.sorted.bam |2013-10-25 02:02:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_sparseassembler.95 |2013-10-25 02:02:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0 |2013-10-25 02:05:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig 100 32 |2013-10-25 02:06:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.cgal |2013-10-25 02:09:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig sparseassembler.95.ale |2013-10-25 02:20:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.sam_0.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig |2013-10-25 02:20:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr |2013-10-25 02:20:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.cmds |2013-10-25 02:20:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.fa |2013-10-25 02:20:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -n 32 -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-25 02:22:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.raw.bam |2013-10-25 02:23:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.raw.bam.sort |2013-10-25 02:24:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.rmdup.bam |2013-10-25 02:24:49| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.header |2013-10-25 02:24:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.header |2013-10-25 02:24:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam |2013-10-25 02:24:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam |2013-10-25 02:24:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam.tmp.24393.smaltmap.* |2013-10-25 02:25:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.perfect |2013-10-25 02:34:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/sparseassembler.95.reapr |2013-10-25 02:36:30| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -k --output_sam_file velvet-sc.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.prob |2013-10-25 02:36:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0.bam |2013-10-25 02:36:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0.sorted |2013-10-25 02:36:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0.sorted.bam |2013-10-25 02:36:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.105 |2013-10-25 02:36:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0 |2013-10-25 02:38:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig 100 32 |2013-10-25 02:38:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.cgal |2013-10-25 02:38:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig velvet-sc.105.ale |2013-10-28 10:25:02|# [VALIDATE] |2013-10-28 10:27:53|# [VALIDATE] |2013-10-28 10:32:20|# [VALIDATE] |2013-10-28 10:46:05|# [VALIDATE] |2013-10-28 10:48:03| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.prob |2013-10-28 10:48:04| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam |2013-10-28 10:48:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.bam |2013-10-28 10:48:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.sorted |2013-10-28 10:48:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.sorted.bam |2013-10-28 10:48:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.105 |2013-10-28 10:48:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam |2013-10-28 10:56:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig 500 32 |2013-10-28 10:56:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.cgal |2013-10-28 10:56:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig velvet-sc.105.ale |2013-10-28 10:56:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig |2013-10-28 10:56:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr |2013-10-28 10:56:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.cmds |2013-10-28 10:56:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.fa |2013-10-28 10:57:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 10:59:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.raw.bam |2013-10-28 11:00:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.raw.bam.sort |2013-10-28 11:02:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.rmdup.bam |2013-10-28 11:02:02| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.header |2013-10-28 11:02:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.header |2013-10-28 11:02:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam |2013-10-28 11:02:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam |2013-10-28 11:02:12| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam.tmp.24178.smaltmap.* |2013-10-28 11:02:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.perfect |2013-10-28 11:12:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.105.reapr |2013-10-28 13:27:57| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.prob |2013-10-28 13:28:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam |2013-10-28 13:29:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.bam |2013-10-28 13:30:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted |2013-10-28 13:31:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam |2013-10-28 13:31:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.125 |2013-10-28 13:31:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam |2013-10-28 13:39:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig 500 32 |2013-10-28 13:40:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.cgal |2013-10-28 13:43:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig velvet-sc.125.ale |2013-10-28 13:47:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig |2013-10-28 14:14:47|# [VALIDATE] |2013-10-28 14:36:54|# [VALIDATE] |2013-10-28 17:13:48| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.prob |2013-10-28 17:13:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam |2013-10-28 17:15:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.bam |2013-10-28 17:16:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted |2013-10-28 17:16:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam |2013-10-28 17:17:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.125 |2013-10-28 17:17:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam |2013-10-28 17:25:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig 500 32 |2013-10-28 17:26:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.cgal |2013-10-28 17:28:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig velvet-sc.125.ale |2013-10-28 17:32:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig |2013-10-28 17:32:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr |2013-10-28 17:32:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.cmds |2013-10-28 17:32:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.fa |2013-10-28 17:33:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 17:36:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.raw.bam |2013-10-28 17:38:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.raw.bam.sort |2013-10-28 17:39:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.rmdup.bam |2013-10-28 17:39:21| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.header |2013-10-28 17:39:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.header |2013-10-28 17:39:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam |2013-10-28 17:39:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam |2013-10-28 17:39:27| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam.tmp.22426.smaltmap.* |2013-10-28 17:39:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.perfect |2013-10-28 17:47:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.125.reapr |2013-10-28 17:49:13| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.prob |2013-10-28 17:49:16| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam |2013-10-28 17:50:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.bam |2013-10-28 17:52:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.sorted |2013-10-28 17:52:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.sorted.bam |2013-10-28 17:52:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.25 |2013-10-28 17:53:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam |2013-10-28 18:01:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig 500 32 |2013-10-28 18:02:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.cgal |2013-10-28 18:05:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig velvet-sc.25.ale |2013-10-28 18:17:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig |2013-10-28 18:17:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr |2013-10-28 18:17:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.cmds |2013-10-28 18:17:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.fa |2013-10-28 18:18:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 18:19:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.raw.bam |2013-10-28 18:21:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.raw.bam.sort |2013-10-28 18:22:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.rmdup.bam |2013-10-28 18:22:09| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.header |2013-10-28 18:22:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.header |2013-10-28 18:22:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam |2013-10-28 18:22:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam |2013-10-28 18:22:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam.tmp.27040.smaltmap.* |2013-10-28 18:22:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.perfect |2013-10-28 18:32:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.25.reapr |2013-10-28 18:34:24| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.prob |2013-10-28 18:34:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam |2013-10-28 18:35:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.bam |2013-10-28 18:37:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.sorted |2013-10-28 18:37:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.sorted.bam |2013-10-28 18:37:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.35 |2013-10-28 18:38:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam |2013-10-28 18:46:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig 500 32 |2013-10-28 18:48:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.cgal |2013-10-28 18:51:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig velvet-sc.35.ale |2013-10-28 19:03:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig |2013-10-28 19:03:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr |2013-10-28 19:03:30| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.cmds |2013-10-28 19:03:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.fa |2013-10-28 19:04:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 19:06:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.raw.bam |2013-10-28 19:08:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.raw.bam.sort |2013-10-28 19:09:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.rmdup.bam |2013-10-28 19:09:09| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.header |2013-10-28 19:09:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.header |2013-10-28 19:09:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam |2013-10-28 19:09:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam |2013-10-28 19:09:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam.tmp.31003.smaltmap.* |2013-10-28 19:09:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.perfect |2013-10-28 19:20:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.35.reapr |2013-10-28 19:23:25| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.prob |2013-10-28 19:23:28| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam |2013-10-28 19:24:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.bam |2013-10-28 19:26:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.sorted |2013-10-28 19:26:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.sorted.bam |2013-10-28 19:27:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.41 |2013-10-28 19:27:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam |2013-10-28 19:36:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig 500 32 |2013-10-28 19:37:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.cgal |2013-10-28 19:40:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig velvet-sc.41.ale |2013-10-28 19:52:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig |2013-10-28 19:53:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr |2013-10-28 19:53:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.cmds |2013-10-28 19:53:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.fa |2013-10-28 19:53:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 19:57:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.raw.bam |2013-10-28 19:58:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.raw.bam.sort |2013-10-28 19:59:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.rmdup.bam |2013-10-28 19:59:40| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.header |2013-10-28 19:59:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.header |2013-10-28 19:59:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam |2013-10-28 19:59:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam |2013-10-28 19:59:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam.tmp.2536.smaltmap.* |2013-10-28 20:00:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.perfect |2013-10-28 20:12:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.41.reapr |2013-10-28 20:14:58| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.prob |2013-10-28 20:15:02| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam |2013-10-28 20:16:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.bam |2013-10-28 20:18:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.sorted |2013-10-28 20:18:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.sorted.bam |2013-10-28 20:18:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.45 |2013-10-28 20:19:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam |2013-10-28 20:27:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig 500 32 |2013-10-28 20:29:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.cgal |2013-10-28 20:32:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig velvet-sc.45.ale |2013-10-28 20:44:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig |2013-10-28 20:44:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr |2013-10-28 20:44:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.cmds |2013-10-28 20:44:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.fa |2013-10-28 20:45:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 20:48:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.raw.bam |2013-10-28 20:49:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.raw.bam.sort |2013-10-28 20:50:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.rmdup.bam |2013-10-28 20:50:47| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.header |2013-10-28 20:50:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.header |2013-10-28 20:50:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam |2013-10-28 20:50:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam |2013-10-28 20:50:54| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam.tmp.6795.smaltmap.* |2013-10-28 20:51:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.perfect |2013-10-28 21:03:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.45.reapr |2013-10-28 21:06:32| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.prob |2013-10-28 21:06:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam |2013-10-28 21:07:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.bam |2013-10-28 21:09:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.sorted |2013-10-28 21:09:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.sorted.bam |2013-10-28 21:10:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.55 |2013-10-28 21:10:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam |2013-10-28 21:19:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig 500 32 |2013-10-28 21:20:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.cgal |2013-10-28 21:23:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig velvet-sc.55.ale |2013-10-28 21:35:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig |2013-10-28 21:35:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr |2013-10-28 21:35:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.cmds |2013-10-28 21:35:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.fa |2013-10-28 21:36:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-28 21:39:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.raw.bam |2013-10-28 21:41:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.raw.bam.sort |2013-10-28 21:42:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.rmdup.bam |2013-10-28 21:42:21| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.header |2013-10-28 21:42:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.header |2013-10-28 21:42:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam |2013-10-28 21:42:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam |2013-10-28 21:42:30| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam.tmp.11065.smaltmap.* |2013-10-28 21:42:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.perfect |2013-10-28 21:54:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.55.reapr |2013-10-29 08:20:40| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.prob |2013-10-29 08:20:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam |2013-10-29 08:21:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.bam |2013-10-29 08:23:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.sorted |2013-10-29 08:23:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.sorted.bam |2013-10-29 08:23:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.65 |2013-10-29 08:24:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam |2013-10-29 08:35:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig 500 32 |2013-10-29 08:36:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.cgal |2013-10-29 08:38:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig velvet-sc.65.ale |2013-10-29 08:41:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig |2013-10-29 08:41:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr |2013-10-29 08:41:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.cmds |2013-10-29 08:41:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.fa |2013-10-29 08:42:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 08:48:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.raw.bam |2013-10-29 08:49:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.raw.bam.sort |2013-10-29 08:50:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.rmdup.bam |2013-10-29 08:50:50| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.header |2013-10-29 08:50:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.header |2013-10-29 08:50:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam |2013-10-29 08:50:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam |2013-10-29 08:50:56| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam.tmp.27392.smaltmap.* |2013-10-29 08:54:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.perfect |2013-10-29 09:05:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.65.reapr |2013-10-29 15:35:47| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.prob |2013-10-29 15:35:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam |2013-10-29 15:37:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.bam |2013-10-29 15:38:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.sorted |2013-10-29 15:38:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.sorted.bam |2013-10-29 15:39:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.75 |2013-10-29 15:39:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam |2013-10-29 15:49:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig 500 32 |2013-10-29 15:50:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.cgal |2013-10-29 15:52:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig velvet-sc.75.ale |2013-10-29 15:58:26| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig |2013-10-29 15:58:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr |2013-10-29 15:58:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.cmds |2013-10-29 15:58:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.fa |2013-10-29 15:59:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 16:05:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.raw.bam |2013-10-29 16:06:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.raw.bam.sort |2013-10-29 16:07:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.rmdup.bam |2013-10-29 16:07:22| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.header |2013-10-29 16:07:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.header |2013-10-29 16:07:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam |2013-10-29 16:07:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam |2013-10-29 16:07:29| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam.tmp.29612.smaltmap.* |2013-10-29 16:10:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.perfect |2013-10-29 16:22:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.75.reapr |2013-10-29 18:18:01| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.prob |2013-10-29 18:18:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam |2013-10-29 18:19:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.bam |2013-10-29 18:20:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.sorted |2013-10-29 18:21:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.sorted.bam |2013-10-29 18:21:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.85 |2013-10-29 18:21:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam |2013-10-29 18:30:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig 500 32 |2013-10-29 18:31:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.cgal |2013-10-29 18:34:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig velvet-sc.85.ale |2013-10-29 18:40:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig |2013-10-29 18:40:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr |2013-10-29 18:40:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.cmds |2013-10-29 18:40:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.fa |2013-10-29 18:41:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 18:48:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.raw.bam |2013-10-29 18:50:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.raw.bam.sort |2013-10-29 18:51:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.rmdup.bam |2013-10-29 18:51:06| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.header |2013-10-29 18:51:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.header |2013-10-29 18:51:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam |2013-10-29 18:51:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam |2013-10-29 18:51:13| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam.tmp.10173.smaltmap.* |2013-10-29 18:52:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.perfect |2013-10-29 19:03:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.85.reapr |2013-10-29 20:16:47| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet-sc.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.prob |2013-10-29 20:16:56| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam |2013-10-29 20:18:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.bam |2013-10-29 20:19:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.sorted |2013-10-29 20:19:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.sorted.bam |2013-10-29 20:20:21| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet-sc.95 |2013-10-29 20:20:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam |2013-10-29 20:30:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig 500 32 |2013-10-29 20:31:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.cgal |2013-10-29 20:33:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig velvet-sc.95.ale |2013-10-29 20:45:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig |2013-10-29 20:45:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr |2013-10-29 20:45:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.cmds |2013-10-29 20:45:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.fa |2013-10-29 20:46:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 20:50:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.raw.bam |2013-10-29 20:51:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.raw.bam.sort |2013-10-29 20:52:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.rmdup.bam |2013-10-29 20:52:43| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.header |2013-10-29 20:52:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.header |2013-10-29 20:52:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam |2013-10-29 20:52:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam |2013-10-29 20:52:50| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam.tmp.20098.smaltmap.* |2013-10-29 20:53:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.perfect |2013-10-29 21:04:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet-sc.95.reapr |2013-10-29 21:06:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.105.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.prob |2013-10-29 21:06:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam |2013-10-29 21:07:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.bam |2013-10-29 21:09:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.sorted |2013-10-29 21:09:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.sorted.bam |2013-10-29 21:10:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.105 |2013-10-29 21:10:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam |2013-10-29 21:19:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig 500 32 |2013-10-29 21:20:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.cgal |2013-10-29 21:23:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig velvet.105.ale |2013-10-29 21:34:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig |2013-10-29 21:34:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr |2013-10-29 21:34:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.cmds |2013-10-29 21:34:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.fa |2013-10-29 21:35:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 21:37:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.raw.bam |2013-10-29 21:39:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.raw.bam.sort |2013-10-29 21:40:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.rmdup.bam |2013-10-29 21:40:18| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.header |2013-10-29 21:40:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.header |2013-10-29 21:40:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam |2013-10-29 21:40:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam |2013-10-29 21:40:25| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam.tmp.24698.smaltmap.* |2013-10-29 21:40:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.perfect |2013-10-29 21:50:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.105.reapr |2013-10-29 21:52:38| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.125.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.prob |2013-10-29 21:52:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam |2013-10-29 21:54:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.bam |2013-10-29 21:55:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.sorted |2013-10-29 21:55:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.sorted.bam |2013-10-29 21:56:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.125 |2013-10-29 21:56:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam |2013-10-29 22:05:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig 500 32 |2013-10-29 22:06:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.cgal |2013-10-29 22:09:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig velvet.125.ale |2013-10-29 22:18:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig |2013-10-29 22:19:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr |2013-10-29 22:19:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.cmds |2013-10-29 22:19:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.fa |2013-10-29 22:19:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 22:21:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.raw.bam |2013-10-29 22:22:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.raw.bam.sort |2013-10-29 22:23:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.rmdup.bam |2013-10-29 22:23:53| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.header |2013-10-29 22:23:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.header |2013-10-29 22:23:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam |2013-10-29 22:24:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam |2013-10-29 22:24:00| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam.tmp.28965.smaltmap.* |2013-10-29 22:24:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.perfect |2013-10-29 22:32:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.125.reapr |2013-10-29 22:41:37| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.25.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.prob |2013-10-29 22:41:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam |2013-10-29 22:42:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.bam |2013-10-29 22:44:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.sorted |2013-10-29 22:44:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.sorted.bam |2013-10-29 22:44:40| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.25 |2013-10-29 22:45:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam |2013-10-29 23:19:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig 500 32 |2013-10-29 23:19:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.cgal |2013-10-29 23:21:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig velvet.25.ale |2013-10-29 23:22:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig |2013-10-29 23:22:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr |2013-10-29 23:22:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.cmds |2013-10-29 23:22:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.fa |2013-10-29 23:24:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-29 23:35:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.raw.bam |2013-10-29 23:37:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.raw.bam.sort |2013-10-29 23:38:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.rmdup.bam |2013-10-29 23:38:06| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.header |2013-10-29 23:38:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.header |2013-10-29 23:38:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam |2013-10-29 23:38:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam |2013-10-29 23:38:15| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam.tmp.2487.smaltmap.* |2013-10-29 23:38:55| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.perfect |2013-10-30 03:58:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.25.reapr |2013-10-30 04:00:41| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.35.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.prob |2013-10-30 04:00:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam |2013-10-30 04:02:03| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.bam |2013-10-30 04:03:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.sorted |2013-10-30 04:03:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.sorted.bam |2013-10-30 04:04:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.35 |2013-10-30 04:04:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam |2013-10-30 04:13:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig 500 32 |2013-10-30 04:15:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.cgal |2013-10-30 04:18:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig velvet.35.ale |2013-10-30 04:30:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig |2013-10-30 04:30:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr |2013-10-30 04:30:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.cmds |2013-10-30 04:30:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.fa |2013-10-30 04:30:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 04:32:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.raw.bam |2013-10-30 04:33:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.raw.bam.sort |2013-10-30 04:34:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.rmdup.bam |2013-10-30 04:34:57| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.header |2013-10-30 04:34:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.header |2013-10-30 04:34:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam |2013-10-30 04:35:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam |2013-10-30 04:35:04| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam.tmp.779.smaltmap.* |2013-10-30 04:35:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.perfect |2013-10-30 04:46:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.35.reapr |2013-10-30 04:49:07| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.41.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.prob |2013-10-30 04:49:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam |2013-10-30 04:50:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.bam |2013-10-30 04:52:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.sorted |2013-10-30 04:52:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.sorted.bam |2013-10-30 04:52:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.41 |2013-10-30 04:53:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam |2013-10-30 05:02:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig 500 32 |2013-10-30 05:03:36| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.cgal |2013-10-30 05:06:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig velvet.41.ale |2013-10-30 05:18:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig |2013-10-30 05:18:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr |2013-10-30 05:18:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.cmds |2013-10-30 05:18:31| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.fa |2013-10-30 05:19:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 05:20:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.raw.bam |2013-10-30 05:22:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.raw.bam.sort |2013-10-30 05:23:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.rmdup.bam |2013-10-30 05:23:15| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.header |2013-10-30 05:23:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.header |2013-10-30 05:23:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam |2013-10-30 05:23:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam |2013-10-30 05:23:22| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam.tmp.4774.smaltmap.* |2013-10-30 05:23:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.perfect |2013-10-30 05:34:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.41.reapr |2013-10-30 05:36:50| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.45.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.prob |2013-10-30 05:36:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam |2013-10-30 05:38:13| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.bam |2013-10-30 05:39:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.sorted |2013-10-30 05:39:58| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.sorted.bam |2013-10-30 05:40:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.45 |2013-10-30 05:40:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam |2013-10-30 05:49:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig 500 32 |2013-10-30 05:51:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.cgal |2013-10-30 05:54:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig velvet.45.ale |2013-10-30 06:06:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig |2013-10-30 06:06:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr |2013-10-30 06:06:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.cmds |2013-10-30 06:06:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.fa |2013-10-30 06:06:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 06:08:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.raw.bam |2013-10-30 06:09:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.raw.bam.sort |2013-10-30 06:10:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.rmdup.bam |2013-10-30 06:10:45| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.header |2013-10-30 06:10:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.header |2013-10-30 06:10:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam |2013-10-30 06:10:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam |2013-10-30 06:10:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam.tmp.8938.smaltmap.* |2013-10-30 06:11:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.perfect |2013-10-30 06:21:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.45.reapr |2013-10-30 06:24:06| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.55.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.prob |2013-10-30 06:24:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam |2013-10-30 06:25:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.bam |2013-10-30 06:27:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.sorted |2013-10-30 06:27:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.sorted.bam |2013-10-30 06:27:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.55 |2013-10-30 06:28:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam |2013-10-30 06:37:04| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig 500 32 |2013-10-30 06:38:27| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.cgal |2013-10-30 06:41:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig velvet.55.ale |2013-10-30 06:53:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig |2013-10-30 06:53:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr |2013-10-30 06:53:20| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.cmds |2013-10-30 06:53:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.fa |2013-10-30 06:53:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 06:55:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.raw.bam |2013-10-30 06:56:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.raw.bam.sort |2013-10-30 06:57:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.rmdup.bam |2013-10-30 06:57:59| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.header |2013-10-30 06:57:59| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.header |2013-10-30 06:58:01| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam |2013-10-30 06:58:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam |2013-10-30 06:58:06| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam.tmp.13146.smaltmap.* |2013-10-30 06:58:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.perfect |2013-10-30 07:09:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.55.reapr |2013-10-30 07:11:28| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.65.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.prob |2013-10-30 07:11:31| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam |2013-10-30 07:12:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.bam |2013-10-30 07:14:32| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.sorted |2013-10-30 07:14:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.sorted.bam |2013-10-30 07:15:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.65 |2013-10-30 07:15:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam |2013-10-30 07:24:33| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig 500 32 |2013-10-30 07:25:56| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.cgal |2013-10-30 07:29:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig velvet.65.ale |2013-10-30 07:41:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig |2013-10-30 07:41:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr |2013-10-30 07:41:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.cmds |2013-10-30 07:41:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.fa |2013-10-30 07:41:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 07:45:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.raw.bam |2013-10-30 07:46:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.raw.bam.sort |2013-10-30 07:47:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.rmdup.bam |2013-10-30 07:47:45| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.header |2013-10-30 07:47:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.header |2013-10-30 07:47:46| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam |2013-10-30 07:47:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam |2013-10-30 07:47:52| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam.tmp.17180.smaltmap.* |2013-10-30 07:48:19| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.perfect |2013-10-30 07:59:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.65.reapr |2013-10-30 08:01:34| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.75.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.prob |2013-10-30 08:01:37| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam |2013-10-30 08:02:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.bam |2013-10-30 08:04:37| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.sorted |2013-10-30 08:04:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.sorted.bam |2013-10-30 08:05:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.75 |2013-10-30 08:05:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam |2013-10-30 08:14:35| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig 500 32 |2013-10-30 08:15:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.cgal |2013-10-30 08:19:10| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig velvet.75.ale |2013-10-30 08:30:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig |2013-10-30 08:30:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr |2013-10-30 08:30:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.cmds |2013-10-30 08:30:52| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.fa |2013-10-30 08:31:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 08:35:16| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.raw.bam |2013-10-30 08:36:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.raw.bam.sort |2013-10-30 08:37:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.rmdup.bam |2013-10-30 08:37:41| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.header |2013-10-30 08:37:41| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.header |2013-10-30 08:37:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam |2013-10-30 08:37:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam |2013-10-30 08:37:48| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam.tmp.21324.smaltmap.* |2013-10-30 08:38:15| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.perfect |2013-10-30 08:48:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.75.reapr |2013-10-30 08:51:21| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.85.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.prob |2013-10-30 08:51:24| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam |2013-10-30 08:52:43| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.bam |2013-10-30 08:54:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.sorted |2013-10-30 08:54:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.sorted.bam |2013-10-30 08:54:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.85 |2013-10-30 08:55:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam |2013-10-30 09:03:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig 500 32 |2013-10-30 09:05:14| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.cgal |2013-10-30 09:08:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig velvet.85.ale |2013-10-30 09:20:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig |2013-10-30 09:20:07| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr |2013-10-30 09:20:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.cmds |2013-10-30 09:20:11| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.fa |2013-10-30 09:20:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 09:22:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.raw.bam |2013-10-30 09:23:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.raw.bam.sort |2013-10-30 09:24:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.rmdup.bam |2013-10-30 09:24:48| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.header |2013-10-30 09:24:48| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.header |2013-10-30 09:24:49| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam |2013-10-30 09:24:54| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam |2013-10-30 09:24:55| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam.tmp.25457.smaltmap.* |2013-10-30 09:25:22| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.perfect |2013-10-30 09:35:44| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.85.reapr |2013-10-30 09:37:44| python /panfs/nbacc1/local/packages/iMetAMOS/LAP/aligner/calc_prob.py -q -k --output_sam_file velvet.95.sam -p 32 -a /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig -n /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.contig.cvg -1 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq -2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq -m 425 -t 32 -I 260 -X 590 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.prob |2013-10-30 09:37:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam_0 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam |2013-10-30 09:39:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools view -bS /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.bam |2013-10-30 09:40:50| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.sorted |2013-10-30 09:40:57| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.sorted.bam |2013-10-30 09:41:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin/FRC --pe-sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.sorted.bam --pe-min-insert 174 --pe-max-insert 665 --genome-size 0 --output frc_velvet.95 |2013-10-30 09:41:53| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/bowtie2convert /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam |2013-10-30 09:50:18| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/align /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig 500 32 |2013-10-30 09:51:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal/cgal /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.cgal |2013-10-30 09:55:05| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src/ALE /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig velvet.95.ale |2013-10-30 10:06:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin/freebayes -C 2 -F 0.51 -O -q 20 -0 -z 0.02 -E 0 -X -u -p 1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.sam.sorted.bam -v /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.vcf -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig |2013-10-30 10:06:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr facheck /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr |2013-10-30 10:06:42| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr smaltmap -x /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.cmds |2013-10-30 10:06:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt index -k 13 -s 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.fa |2013-10-30 10:07:23| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt sample -u 1000 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.smalt_sample /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq |2013-10-30 10:09:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/smalt map -n 32 -r 0 -x -y 0.5 -g /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.smalt_sample -f samsoft /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.smalt_index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq | awk '$1!~/^#/' | /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -S -T /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.fa -b - > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.raw.bam |2013-10-30 10:11:08| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools sort /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.raw.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.raw.bam.sort |2013-10-30 10:12:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools rmdup /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.raw.bam.sort.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.rmdup.bam |2013-10-30 10:12:25| echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.header |2013-10-30 10:12:25| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools view -H /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.rmdup.bam >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.header |2013-10-30 10:12:39| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools reheader /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.header /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.rmdup.bam > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam |2013-10-30 10:12:45| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/src/samtools index /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam |2013-10-30 10:12:45| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam.tmp.29479.smaltmap.* |2013-10-30 10:13:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr perfectmap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq 419 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.perfect |2013-10-30 10:24:02| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/REAPR/reapr pipeline /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr.bam /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/velvet.95.reapr |2013-10-30 10:24:02| mkdir -p /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/recruit |2013-10-30 10:29:29| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/mgcat -M -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig -d /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//refseq -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/recruit -p 32 |2013-10-30 10:29:30| cat /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB/refseq/Rhodobacter_sphaeroides_2_4_1_uid57653.fna |awk -F "|" '{if (match($1, ">")) { if (NF >= 2) { line=$1"_"$2; for (i=3; i<= NF; i++) { line=line" "$i; } } else { line = $1; } print line; } else {print $0; }}' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.fasta |2013-10-30 11:09:16| /panfs/nbacc1/local/packages/iMetAMOS/quast/metaquast.py --est-ref-size 0 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/quast -R /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.fasta -T 32 -l "abyss_25,abyss_35,abyss_41,abyss_45,abyss_55,abyss_65,abyss_75,abyss_85,abyss_95,idba-ud_105,idba-ud_25,idba-ud_35,idba-ud_41,idba-ud_45,idba-ud_55,idba-ud_65,idba-ud_75,idba-ud_85,idba-ud_95,masurca_105,masurca_125,masurca_25,masurca_35,masurca_41,masurca_45,masurca_55,masurca_65,masurca_75,masurca_85,masurca_95,mira_105,mira_125,mira_25,mira_35,mira_41,mira_45,mira_55,mira_65,mira_75,mira_85,mira_95,ray_105,ray_125,ray_25,ray_35,ray_41,ray_45,ray_55,ray_65,ray_75,ray_85,ray_95,sga_105,sga_125,sga_25,sga_35,sga_41,sga_45,sga_55,sga_65,sga_75,sga_85,sga_95,soapdenovo2_25,soapdenovo2_35,soapdenovo2_41,soapdenovo2_45,soapdenovo2_55,soapdenovo2_65,soapdenovo2_75,soapdenovo2_85,soapdenovo2_95,spades_105,spades_125,spades_25,spades_35,spades_41,spades_45,spades_55,spades_65,spades_75,spades_85,spades_95,sparseassembler_105,sparseassembler_125,sparseassembler_25,sparseassembler_35,sparseassembler_41,sparseassembler_45,sparseassembler_55,sparseassembler_65,sparseassembler_75,sparseassembler_85,sparseassembler_95,velvet-sc_105,velvet-sc_125,velvet-sc_25,velvet-sc_35,velvet-sc_41,velvet-sc_45,velvet-sc_55,velvet-sc_65,velvet-sc_75,velvet-sc_85,velvet-sc_95,velvet_105,velvet_125,velvet_25,velvet_35,velvet_41,velvet_45,velvet_55,velvet_65,velvet_75,velvet_85,velvet_95" /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.125.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.25.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.35.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.45.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.55.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.65.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.75.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.85.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.95.asm.contig |2013-10-30 11:09:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |2013-10-30 11:09:17| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final |2013-10-30 11:09:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.tigr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr |2013-10-30 11:09:18| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt |2013-10-30 11:09:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg |2013-10-30 11:09:19| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.afg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.afg |2013-10-30 11:09:19| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-10-30 11:09:19|# [FINDORFS] |2013-10-30 11:09:20| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-30 11:09:20| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 15:43:44|# [VALIDATE] |2013-10-31 15:53:33|# [ASSEMBLE] |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.run |2013-10-31 15:53:33| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.run |2013-10-31 15:53:34| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/abyss/bin/abyss-pe k=41 name=abyss.41 lib='lib1' mp='' np=32 lib1='/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.1.fastq /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.2.fastq' |2013-10-31 15:53:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig |2013-10-31 15:53:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41-contigs.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.asm.contig |2013-10-31 15:53:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41-contigs.fa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/abyss.41.linearize.scaffolds.final |2013-10-31 15:54:28|# [ASSEMBLE] |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/spades.41.run |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/mira.41.run |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/soapdenovo2.41.run |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet.41.run |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sga.41.run |2013-10-31 15:54:28| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/idba-ud.41.run |2013-10-31 15:54:29| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.41.run |2013-10-31 15:54:29| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.41.run |2013-10-31 15:54:29| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/sparseassembler.41.run |2013-10-31 15:54:29| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/ray.41.run |2013-10-31 15:55:52|# [VALIDATE] |2013-10-31 15:57:03|# [MAPREADS] |2013-10-31 16:22:33|# [VALIDATE] |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.asm.tigr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/velvet-sc.105.afg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.afg |2013-10-31 16:22:34| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-10-31 16:22:34|# [FINDORFS] |2013-10-31 16:22:34| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 16:22:34| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 16:50:13|# [VALIDATE] |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.asm.tigr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg |2013-10-31 16:50:14| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-10-31 16:50:14|# [FINDORFS] |2013-10-31 16:50:14| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 16:50:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 16:50:17| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka --prefix proba --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 17:17:07|# [VALIDATE] |2013-10-31 17:17:08| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |2013-10-31 17:17:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final |2013-10-31 17:17:09| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.tigr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr |2013-10-31 17:17:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt |2013-10-31 17:17:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg |2013-10-31 17:17:10| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-10-31 17:17:10|# [FINDORFS] |2013-10-31 17:17:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 17:17:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 18:24:38| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka --prefix proba --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-10-31 18:24:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka/proba.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.fna |2013-10-31 18:24:38| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.faa |2013-10-31 18:24:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.gene.cvg |2013-10-31 18:24:38| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.gene.map |2013-10-31 18:24:38| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna |2013-10-31 18:24:39| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna |2013-10-31 18:24:39| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna.bnk |2013-10-31 18:24:41| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna.bnk |2013-10-31 18:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa |2013-10-31 18:24:42| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa |2013-10-31 18:24:42| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa.bnk |2013-10-31 18:24:44| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa.bnk |2013-10-31 18:24:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg |2013-10-31 18:24:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg |2013-10-31 18:24:44| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map |2013-10-31 18:24:44| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map |2013-10-31 18:24:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.faa |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.fna |2013-10-31 18:24:45| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.faa |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindRepeats/in/proba.fna |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindRepeats/in/proba.faa |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.fna |2013-10-31 18:24:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.faa |2013-10-31 18:24:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.badmates /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.badmates |2013-10-31 18:24:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.hdr |2013-10-31 18:24:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.mappedmates |2013-10-31 18:24:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mates_in_diff_contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.mates_in_diff_contigs |2013-10-31 18:24:48| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads |2013-10-31 18:24:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta |2013-10-31 18:24:50|# [FINDREPEATS] |2013-10-31 18:24:50| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findrepeats.skip |2013-10-31 18:24:51|# [ANNOTATE] |2013-10-31 18:24:51| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots |2013-10-31 18:24:51| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.asm.contig |2013-10-31 18:24:52| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/ |2013-10-31 18:24:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits |2013-10-31 18:24:52| rm -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/*.hits |2013-10-31 18:24:52| rm -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/*.epsilon-nb_results.txt |2013-10-31 18:24:52| rm -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/*.phymm.out |2013-10-31 18:24:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/lib1.unaligned.fasta |2013-10-31 18:24:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/lib1.unaligned.fasta |2013-10-31 18:35:28| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 32 -db /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//kraken --output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.intermediate.ctg.hits /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.asm.contig --preload |2013-10-31 18:44:06| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 32 -db /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//kraken --output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.intermediate.lib1.hits /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/lib1.unaligned.fasta --preload |2013-10-31 18:44:06| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits |2013-10-31 18:44:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.intermediate.ctg.hits >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits |2013-10-31 18:44:06| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.intermediate.lib1.hits >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits |2013-10-31 18:44:43| perl /panfs/nbacc1/local/packages/iMetAMOS/Utilities/perl/ImportKraken.pl -l -c -i -f /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.asm.contig:/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits:/panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt:genus |2013-10-31 18:44:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/in/proba.hits |2013-10-31 18:44:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.hits |2013-10-31 18:44:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/in/proba.hits |2013-10-31 18:44:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.hits /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.hits |2013-10-31 18:44:48|# [FUNCTIONALANNOTATION] |2013-10-31 19:08:00| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa -d /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//uniprot_sprot.fasta -a 32 -e 0.001 -m 8 -b 1 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/blast.out |2013-10-31 19:08:04| /panfs/nbacc1/local/packages/iMetAMOS/KronaTools/bin/ktImportEC -l /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/krona.ec.input |2013-11-04 12:24:58|# [VALIDATE] |2013-11-04 12:24:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |2013-11-04 12:24:58| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final |2013-11-04 12:24:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.asm.tigr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr |2013-11-04 12:24:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt |2013-11-04 12:24:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg |2013-11-04 12:24:59| rm /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-11-04 12:24:59|# [FINDORFS] |2013-11-04 12:24:59| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-11-04 12:24:59| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-11-04 13:34:09| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka --prefix proba --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-11-04 13:34:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka/proba.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.fna |2013-11-04 13:34:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.prokka/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.faa |2013-11-04 13:34:10| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.gene.cvg |2013-11-04 13:34:10| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.ctg.gene.map |2013-11-04 13:34:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna |2013-11-04 13:34:10| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.fna > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna |2013-11-04 13:34:10| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna.bnk |2013-11-04 13:34:11| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna.bnk |2013-11-04 13:34:11| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa |2013-11-04 13:34:12| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.faa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa |2013-11-04 13:34:12| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa.bnk |2013-11-04 13:34:13| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa.bnk |2013-11-04 13:34:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg |2013-11-04 13:34:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.gene.cvg > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg |2013-11-04 13:34:13| rm -r /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map |2013-11-04 13:34:13| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba*.gene.map > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.map |2013-11-04 13:34:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.faa |2013-11-04 13:34:13| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.fna |2013-11-04 13:34:14| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findorfs.ok |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.faa |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindRepeats/in/proba.fna |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindRepeats/in/proba.faa |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.fna |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/in/proba.faa |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.badmates /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.badmates |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.hdr /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.hdr |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mappedmates /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.mappedmates |2013-11-04 13:34:14| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.mates_in_diff_contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1.mates_in_diff_contigs |2013-11-04 13:34:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads |2013-11-04 13:34:15| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.95.lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta |2013-11-04 13:34:16|# [FINDREPEATS] |2013-11-04 13:34:16| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findrepeats.skip |2013-11-04 13:34:17|# [FUNCTIONALANNOTATION] |2013-11-04 13:57:24| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa -d /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//uniprot_sprot.fasta -a 32 -e 0.001 -m 8 -b 1 > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/blast.out |2013-11-04 13:57:26| /panfs/nbacc1/local/packages/iMetAMOS/KronaTools/bin/ktImportEC -l /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/krona.ec.input |2013-11-04 13:57:27|# [SCAFFOLD] |2013-11-04 13:57:27| rm -rf /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk |2013-11-04 14:01:17| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -Q /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/lib1.seq -i --min 200 --max 800 --libname lib1 -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk |2013-11-04 14:01:48| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/toAmos_new -c /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.tigr -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk |2013-11-04 14:01:53| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.contigs |2013-11-04 14:01:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final |2013-11-04 14:01:53| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.scaffolds.final |2013-11-04 14:01:53| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/scaffold.skip |2013-11-04 14:01:54|# [FINDSCAFFOLDORFS] |2013-11-04 15:03:47| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --outdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindScaffoldORFS/out/prokka --prefix proba --force /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final |2013-11-04 15:03:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindScaffoldORFS/out/prokka/proba.ffn /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindScaffoldORFS/out/proba.fna |2013-11-04 15:03:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindScaffoldORFS/out/prokka/proba.faa /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindScaffoldORFS/out/proba.faa |2013-11-04 15:03:48|# [ABUNDANCE] |2013-11-04 15:03:48| ln -s /panfs/nbacc1/local/packages/iMetAMOS/Utilities/DB//markers.pfasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/markers.pfasta |2013-11-04 15:03:51| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/formatdb -p T -i /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/markers.pfasta |2013-11-04 15:05:12| /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa -d /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 32 -o /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.blastp |2013-11-04 15:05:15| perl /panfs/nbacc1/local/packages/iMetAMOS/Utilities/perl/metaphyler_contigs.pl /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.blastp proba /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.gene.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out /panfs/nbacc1/local/packages/iMetAMOS/Utilities |2013-11-04 15:05:26| perl /panfs/nbacc1/local/packages/iMetAMOS/Utilities/perl/ImportMetaPhyler.pl -l -c -v -i -p /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.taxprof.pct.txt:genus |2013-11-04 15:05:27|# [PROPAGATE] |2013-11-04 15:05:27| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.annots |2013-11-04 15:05:27| cat /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters |2013-11-04 15:05:27| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/propagate.skip |2013-11-04 15:05:28| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.clusters |2013-11-04 21:18:57|# [CLASSIFY] |2013-11-04 21:19:03| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/shuffleBank -c -e -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk -p ctg -eid -E /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/contig.fofn |2013-11-04 21:28:41| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk -eid -E /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/read.fofn |2013-11-04 21:37:13| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/shuffleBank -r -f -e -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk -eid -E /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/read.fofn |2013-11-04 21:37:14| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.fna.bnk -p fna -eid -E /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/orf.fofn |2013-11-04 21:37:15| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/out/proba.faa.bnk -p faa -eid -E /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/orf.fofn |2013-11-04 21:37:18| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. SizeFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig |awk '{if ($NF >= 100) { print $1} }' > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.ctg.iids |2013-11-04 21:37:18| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.read.iids |2013-11-04 21:37:25| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. SizeFasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta |awk '{if ($NF >= 100) { print $1} }' >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.read.iids |2013-11-04 21:38:14| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. SubFile /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.ctg.iids /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads 1 >> /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.read.iids |2013-11-04 21:38:38| java -cp /panfs/nbacc1/local/packages/iMetAMOS/Utilities/java:. SubFile /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.read.iids /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.reads.clusters > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/proba.read.contaminant.clusters |2013-11-04 21:38:38| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out/contaminant.true |2013-11-04 21:38:41|# [POSTPROCESS] |2013-11-04 21:38:41| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-04 21:38:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-04 21:38:41| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-04 21:38:41| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-04 21:38:41| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-04 21:38:41| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-04 21:38:42| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/lap.scores |2013-11-04 21:38:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.lap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/lap.scores |2013-11-04 21:38:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/best.asm |2013-11-04 21:38:43| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.asm.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/best.asm |2013-11-04 21:38:43| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/ref.asm |2013-11-04 21:38:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ref.asm |2013-11-04 21:38:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/quast |2013-11-04 21:38:44| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/quast/combined_quast_output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/quast |2013-11-04 21:38:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-04 21:38:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba_report.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-04 21:38:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-04 21:38:44| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-04 21:38:44| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-04 21:38:45| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.reads.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-04 21:38:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.annots |2013-11-04 21:38:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.reads.annots |2013-11-04 21:38:48| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.classify.txt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/. |2013-11-04 21:38:48| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.scf.fa |2013-11-04 21:38:49| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.fa |2013-11-04 21:38:49| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ |2013-11-04 21:38:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-04 21:38:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-04 21:38:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-04 21:38:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-04 21:38:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-04 21:38:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-04 21:38:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-04 21:38:49| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-04 21:38:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-04 21:38:49| mkdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-04 21:38:50| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/*.fastqc /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-04 21:38:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-04 21:38:50| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/ec.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-04 21:38:51| perl -I /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/lib /panfs/nbacc1/local/packages/iMetAMOS/Utilities/perl/statistics.pl /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.scf.fa > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/asmstats.out |2013-11-04 21:39:16| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/analyze-read-depth -x 2 /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.bnk > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/covstats.out |2013-11-04 21:39:36| /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin/astats /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.bnk > /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/stats.out |2013-11-06 10:01:19|# [MAPREADS] |2013-11-06 10:04:54|# [FINDORFS] |2013-11-06 10:04:54| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-11-06 10:04:54| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-11-06 10:15:10|# [FINDORFS] |2013-11-06 10:15:10| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-11-06 10:15:10| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/masurca.105.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/masurca.105.asm.contig |2013-11-06 10:17:12|# [FINDORFS] |2013-11-06 10:17:12| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-11-06 10:17:12| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.asm.contig /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FindORFS/in/proba.asm.contig |2013-11-06 10:42:45|# [FINDREPEATS] |2013-11-06 10:42:45| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findrepeats.skip |2013-11-06 10:42:46|# [POSTPROCESS] |2013-11-06 10:42:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:42:46| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:42:46| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:42:47| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/lap.scores |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.lap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/lap.scores |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/best.asm |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.asm.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/best.asm |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/ref.asm |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ref.asm |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/quast |2013-11-06 10:42:47| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/quast/combined_quast_output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/quast |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba_report.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:42:47| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:42:47| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.reads.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:42:49| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.annots |2013-11-06 10:42:50| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.reads.annots |2013-11-06 10:42:51| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.classify.txt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/. |2013-11-06 10:42:51| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.scf.fa |2013-11-06 10:42:51| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.fa |2013-11-06 10:42:51| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:42:52| mkdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:42:52| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/*.fastqc /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:42:52| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-06 10:42:52| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/ec.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-06 10:56:06|# [FINDREPEATS] |2013-11-06 10:56:06| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findrepeats.skip |2013-11-06 10:56:07|# [POSTPROCESS] |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:56:07| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/lap.scores |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.lap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/lap.scores |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/best.asm |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.asm.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/best.asm |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/ref.asm |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ref.asm |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/quast |2013-11-06 10:56:07| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/quast/combined_quast_output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/quast |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba_report.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:56:07| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:56:07| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.reads.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:56:08| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.annots |2013-11-06 10:56:09| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.reads.annots |2013-11-06 10:56:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.classify.txt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/. |2013-11-06 10:56:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.scf.fa |2013-11-06 10:56:10| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.fa |2013-11-06 10:56:10| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ |2013-11-06 10:56:10| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:56:11| mkdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:56:11| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/*.fastqc /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:56:11| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-06 10:56:11| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/ec.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-06 10:59:34|# [FINDREPEATS] |2013-11-06 10:59:34| touch /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Logs/findrepeats.skip |2013-11-06 10:59:35|# [POSTPROCESS] |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/report.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:59:35| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Classify/out /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/lap.scores |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.lap /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/lap.scores |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/best.asm |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.asm.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/best.asm |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/ref.asm |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/proba.ref.selected /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ref.asm |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postporocess/out/quast |2013-11-06 10:59:35| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Validate/out/quast/combined_quast_output /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/quast |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba_report.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/kmergenie_report.html |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.annots |2013-11-06 10:59:35| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:59:35| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Annotate/out/proba.reads.annots /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.original.reads.annots |2013-11-06 10:59:36| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.annots |2013-11-06 10:59:37| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.propagated.reads.annots |2013-11-06 10:59:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Abundance/out/proba.classify.txt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/. |2013-11-06 10:59:38| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.linearize.scaffolds.final /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.scf.fa |2013-11-06 10:59:39| cp /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/out/proba.contigs /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.fa |2013-11-06 10:59:39| ln -s /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Scaffold/in/proba.bnk /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/ |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.lib1contig.reads /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.contig.reads |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/lib1.unaligned.fasta /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.lib1.unaligned.fasta |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cnt /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cnt |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Assemble/out/proba.contig.cvg /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/proba.ctg.cvg |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:59:39| mkdir /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/genus.classified /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/genus.classified |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/annotate.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Annotate.html |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/abundance.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/Abundance.html |2013-11-06 10:59:39| mv /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Preprocess/out/*.fastqc /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/in/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.in.clusters |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Propagate/out/proba.clusters /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/propagate.out.clusters |2013-11-06 10:59:39| unlink /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html |2013-11-06 10:59:39| ln /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/FunctionalAnnotation/out/ec.krona.html /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate/Postprocess/out/html/FunctionalAnnotation.html