doExtendClearRanges = 2 cgwOutputIntermediate = 1 ----------------------------------------START Fri Jan 30 14:25:16 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore.BUILDING -T -F -L -E /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore.errorLog /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/cpqg.frg > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore.err 2>&1 ----------------------------------------END Fri Jan 30 14:25:23 2009 (7 seconds) Backing up the gkpStore to beforeTrimming. ----------------------------------------START Fri Jan 30 14:25:23 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/initialTrim -log /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.initialTrimLog -frg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.initialTrim.report 2> /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.initialTrim.err ----------------------------------------END Fri Jan 30 14:25:24 2009 (1 seconds) Backing up the gkpStore to beforePrefixDelete. ----------------------------------------START Fri Jan 30 14:25:25 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/prefixDelete -log /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.prefixDeleteLog -frg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.prefixDelete.report 2> /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.prefixDelete.err ----------------------------------------END Fri Jan 30 14:25:25 2009 (0 seconds) /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------START Fri Jan 30 14:25:25 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl -B -C -v -m 22 -memory 800 -threads 1 -c 0 -L 500 -s /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore:obt -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/cpqg-C-ms22-cm0 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/meryl.out 2>&1 ----------------------------------------END Fri Jan 30 14:25:50 2009 (25 seconds) ----------------------------------------START Fri Jan 30 14:25:50 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl -Dt -n 500 -s /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/cpqg-C-ms22-cm0 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/cpqg.nmers.ovl.fasta /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------END Fri Jan 30 14:25:51 2009 (1 seconds) /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------START Fri Jan 30 14:25:51 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl -Dt -n 1000 -s /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/cpqg-C-ms22-cm0 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-mercounts/cpqg.nmers.obt.fasta /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------END Fri Jan 30 14:25:52 2009 (1 seconds) ----------------------------------------START Fri Jan 30 14:25:52 2009 /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim-overlap/overlap.sh 1 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim-overlap/overlap.0001.out 2>&1 ----------------------------------------END Fri Jan 30 14:27:28 2009 (96 seconds) ----------------------------------------START Fri Jan 30 14:27:28 2009 find /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim-overlap -follow -name \*ovb.gz -print > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore.list ----------------------------------------END Fri Jan 30 14:27:28 2009 (0 seconds) ----------------------------------------START Fri Jan 30 14:27:28 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -O -c /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore.BUILDING -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -M 1024 -L /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore.list > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore.err 2>&1 ----------------------------------------END Fri Jan 30 14:27:44 2009 (16 seconds) ----------------------------------------START Fri Jan 30 14:27:44 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/consolidate -ovs /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.ovl.consolidated /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/consolidate: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/consolidate: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/consolidate: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------END Fri Jan 30 14:27:49 2009 (5 seconds) Backing up the gkpStore to beforeTrimMerge. ----------------------------------------START Fri Jan 30 14:27:49 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/merge-trimming -log /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.mergeLog -frg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -ovl /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.ovl.consolidated > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.merge.err 2>&1 ----------------------------------------END Fri Jan 30 14:27:50 2009 (1 seconds) Backing up the gkpStore to beforeChimera. ----------------------------------------START Fri Jan 30 14:27:50 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/chimera -gkp /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -ovs /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.obtStore -summary /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.chimera.summary -report /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.chimera.report > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./0-overlaptrim/cpqg.chimera.err 2>&1 ----------------------------------------END Fri Jan 30 14:27:54 2009 (4 seconds) Backing up the gkpStore to afterTrimming. ----------------------------------------START Fri Jan 30 14:27:54 2009 /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./1-overlapper/overlap.sh 1 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./1-overlapper/overlap.0001.out 2>&1 ----------------------------------------END Fri Jan 30 14:29:08 2009 (74 seconds) ----------------------------------------START Fri Jan 30 14:29:08 2009 find /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./1-overlapper -name \*ovb.gz -print > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore.list ----------------------------------------END Fri Jan 30 14:29:08 2009 (0 seconds) ----------------------------------------START Fri Jan 30 14:29:08 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -c /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore.BUILDING -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -M 1024 -L /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore.list > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore.err 2>&1 ----------------------------------------END Fri Jan 30 14:29:15 2009 (7 seconds) ----------------------------------------START CONCURRENT Fri Jan 30 14:29:15 2009 sh /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/frgcorr.sh 1 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/0001.err 2>&1 ----------------------------------------END CONCURRENT Fri Jan 30 14:29:32 2009 (17 seconds) ----------------------------------------START Fri Jan 30 14:29:32 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cat-corrects -L /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cat-corrects.frgcorrlist -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cpqg.frgcorr > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cat-corrects.err 2>&1 ----------------------------------------END Fri Jan 30 14:29:32 2009 (0 seconds) ----------------------------------------START CONCURRENT Fri Jan 30 14:29:32 2009 sh /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/ovlcorr.sh 1 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/0001.err 2>&1 ----------------------------------------END CONCURRENT Fri Jan 30 14:29:44 2009 (12 seconds) ----------------------------------------START Fri Jan 30 14:29:44 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cat-erates -L /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cat-erates.eratelist -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cpqg.erates > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cat-erates.err 2>&1 ----------------------------------------END Fri Jan 30 14:29:44 2009 (0 seconds) ----------------------------------------START Fri Jan 30 14:29:44 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -u /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/cpqg.erates> /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./3-overlapcorrection/overlapStore-update-erates.err 2>&1 ----------------------------------------END Fri Jan 30 14:29:45 2009 (1 seconds) /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------START Fri Jan 30 14:29:45 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/unitigger -k -B 75000 -d 1 -x 1 -z 10 -j 5 -U 1 -e 0.015 -F /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./4-unitigger/cpqg -I /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.ovlStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./4-unitigger/unitigger.err 2>&1 ----------------------------------------END Fri Jan 30 14:30:00 2009 (15 seconds) ----------------------------------------START Fri Jan 30 14:30:00 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -P /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg.partFile /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg.partitioned.err 2>&1 ----------------------------------------END Fri Jan 30 14:30:03 2009 (3 seconds) ----------------------------------------START CONCURRENT Fri Jan 30 14:30:03 2009 sh /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/consensus.sh 1 > /dev/null 2>&1 ----------------------------------------END CONCURRENT Fri Jan 30 14:31:56 2009 (113 seconds) ----------------------------------------START Fri Jan 30 14:31:56 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -j 1 -k 5 -r 5 -s 2 -S 0 -z -m 100 -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/cpqg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg_001.cgi > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/cgw.out 2>&1 ----------------------------------------END Fri Jan 30 14:32:47 2009 (51 seconds) ----------------------------------------START Fri Jan 30 14:32:47 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -a -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -E /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/gkp.distupdate.err /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/stat/scaffold_final.distupdate.dst /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/stat/contig_final.distupdate.dst > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./6-clonesize/cgw.distupdate.err 2>&1 ----------------------------------------END Fri Jan 30 14:32:47 2009 (0 seconds) ----------------------------------------START Fri Jan 30 14:32:47 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -j 1 -k 5 -r 5 -s 0 -S 0 -z -m 100 -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-0-CGW/cpqg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg_001.cgi > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-0-CGW/cgw.out 2>&1 ----------------------------------------END Fri Jan 30 14:33:09 2009 (22 seconds) Found 34 scaffolds in 7-1-ECR checkpoint number 4. ----------------------------------------START Fri Jan 30 14:33:09 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/extendClearRanges -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -n 4 -c cpqg -b 00 -e 34 -i 1 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-1-ECR/extendClearRanges-scaffold.00.err 2>&1 ----------------------------------------END Fri Jan 30 14:33:14 2009 (5 seconds) ----------------------------------------START Fri Jan 30 14:33:14 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -y -R 5 -N 3 -j 1 -k 5 -r 5 -s 0 -S 0 -z -m 100 -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-2-CGW/cpqg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg_001.cgi > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-2-CGW/cgw.out 2>&1 ----------------------------------------END Fri Jan 30 14:33:20 2009 (6 seconds) Found 18 scaffolds in 7-3-ECR checkpoint number 10. ----------------------------------------START Fri Jan 30 14:33:21 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/extendClearRanges -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -n 10 -c cpqg -b 00 -e 18 -i 2 > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-3-ECR/extendClearRanges-scaffold.00.err 2>&1 ----------------------------------------END Fri Jan 30 14:33:23 2009 (2 seconds) ----------------------------------------START Fri Jan 30 14:33:23 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -y -R 11 -N 3 -j 1 -k 5 -r 5 -s 2 -z -m 100 -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-4-CGW/cpqg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./5-consensus/cpqg_001.cgi > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-4-CGW/cgw.out 2>&1 ----------------------------------------END Fri Jan 30 14:34:15 2009 (52 seconds) ----------------------------------------START Fri Jan 30 14:34:16 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/PartitionSDB -all -seqstore /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-CGW/cpqg.SeqStore -version 20 -fragsper 75000 -input /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-CGW/cpqg.cgw_contigs > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./8-consensus/partitionSDB.err 2>&1 ----------------------------------------END Fri Jan 30 14:34:17 2009 (1 seconds) ----------------------------------------START Fri Jan 30 14:34:17 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -P /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./8-consensus/FragPartition.txt /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./8-consensus/cpqg.partitioned.err 2>&1 ----------------------------------------END Fri Jan 30 14:34:20 2009 (3 seconds) ----------------------------------------START CONCURRENT Fri Jan 30 14:34:20 2009 sh /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./8-consensus/consensus.sh 1 > /dev/null 2>&1 ----------------------------------------END CONCURRENT Fri Jan 30 14:35:51 2009 (91 seconds) ----------------------------------------START Fri Jan 30 14:35:51 2009 cat /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-CGW/cpqg.cgw /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./8-consensus/cpqg.cns_contigs.*[0-9] /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-CGW/cpqg.cgw_scaffolds | /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/terminator -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -o /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/terminator.err 2>&1 ----------------------------------------END Fri Jan 30 14:35:53 2009 (2 seconds) ----------------------------------------START Fri Jan 30 14:35:53 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/asmOutputFasta -p /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.asm /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/asmOutputFasta: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/asmOutputFasta: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/asmOutputFasta: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 All output successfully written. ----------------------------------------END Fri Jan 30 14:35:55 2009 (2 seconds) ----------------------------------------START Fri Jan 30 14:35:55 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/dumpSingletons -g /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./cpqg.gkpStore -c /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./7-CGW/cpqg -n 20 -S > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.singleton.fasta 2> /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/dumpSingletons.err ----------------------------------------END Fri Jan 30 14:35:55 2009 (0 seconds) ----------------------------------------START Fri Jan 30 14:35:55 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/buildPosMap -o cpqg < /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.asm /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/buildPosMap: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/buildPosMap: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/buildPosMap: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------END Fri Jan 30 14:35:56 2009 (1 seconds) ----------------------------------------START Fri Jan 30 14:35:56 2009 sort -k2n -T /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.sorted &&/fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 0 -max 3000 < /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.sorted > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.histogram1 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 3001 -max 10000 < /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.sorted > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.histogram2 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 10001 -max 1000000 < /fs/sza smg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.sorted > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.histogram3 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 1000001 < /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.sorted > /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.posmap.frgscf.histogram4 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_OVL_ERROR_RATE set to 0.06 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CGW_ERROR_RATE set to 0.10 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth: AS_configure()-- AS_CNS_ERROR_RATE set to 0.06 ----------------------------------------END Fri Jan 30 14:35:57 2009 (1 seconds) ----------------------------------------START Fri Jan 30 14:35:57 2009 /usr/bin/env perl /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/caqc.pl -euid -metrics /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator/cpqg.asm Cannot open /fs/szasmg2/Culex_pipiens_symbiont/2009_0130_WGA-wgs-e.20/./9-terminator//cpqg.frg at /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/caqc.pl line 655. ----------------------------------------END Fri Jan 30 14:35:57 2009 (0 seconds) ERROR: Failed with signal INT (2) The Cleaner has arrived. Doing 'none'.