----------------------------------------START Wed Jan 28 11:08:37 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore.BUILDING -T -F -L -E /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore.errorLog /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/bt.frg > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore.err 2>&1 ----------------------------------------END Wed Jan 28 11:08:43 2009 (6 seconds) Backing up the gkpStore to beforeTrimming. ----------------------------------------START Wed Jan 28 11:08:43 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/initialTrim -log /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.initialTrimLog -frg /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.initialTrim.report 2> /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.initialTrim.err ----------------------------------------END Wed Jan 28 11:08:44 2009 (1 seconds) Backing up the gkpStore to beforePrefixDelete. ----------------------------------------START Wed Jan 28 11:08:44 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/prefixDelete -log /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.prefixDeleteLog -frg /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.prefixDelete.report 2> /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.prefixDelete.err ----------------------------------------END Wed Jan 28 11:08:44 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 Wed Jan 28 11:08:44 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/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore:obt -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/bt-C-ms22-cm0 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/meryl.out 2>&1 ----------------------------------------END Wed Jan 28 11:09:05 2009 (21 seconds) ----------------------------------------START Wed Jan 28 11:09:05 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl -Dt -n 500 -s /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/bt-C-ms22-cm0 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/bt.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 Wed Jan 28 11:09:06 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 Wed Jan 28 11:09:06 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/meryl -Dt -n 1000 -s /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/bt-C-ms22-cm0 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-mercounts/bt.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 Wed Jan 28 11:09:08 2009 (2 seconds) ----------------------------------------START Wed Jan 28 11:09:08 2009 /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim-overlap/overlap.sh 1 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim-overlap/overlap.0001.out 2>&1 ----------------------------------------END Wed Jan 28 11:10:11 2009 (63 seconds) ----------------------------------------START Wed Jan 28 11:10:11 2009 find /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim-overlap -follow -name \*ovb.gz -print > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore.list ----------------------------------------END Wed Jan 28 11:10:11 2009 (0 seconds) ----------------------------------------START Wed Jan 28 11:10:11 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -O -c /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore.BUILDING -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -M 1024 -L /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore.list > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:21 2009 (10 seconds) ----------------------------------------START Wed Jan 28 11:10:21 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/consolidate -ovs /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.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 Wed Jan 28 11:10:22 2009 (1 seconds) Backing up the gkpStore to beforeTrimMerge. ----------------------------------------START Wed Jan 28 11:10:22 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/merge-trimming -log /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.mergeLog -frg /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -ovl /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.ovl.consolidated > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.merge.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:23 2009 (1 seconds) Backing up the gkpStore to beforeChimera. ----------------------------------------START Wed Jan 28 11:10:23 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/chimera -gkp /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -ovs /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.obtStore -summary /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.chimera.summary -report /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.chimera.report > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./0-overlaptrim/bt.chimera.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:25 2009 (2 seconds) Backing up the gkpStore to afterTrimming. ----------------------------------------START Wed Jan 28 11:10:26 2009 /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./1-overlapper/overlap.sh 1 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./1-overlapper/overlap.0001.out 2>&1 ----------------------------------------END Wed Jan 28 11:10:48 2009 (22 seconds) ----------------------------------------START Wed Jan 28 11:10:48 2009 find /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./1-overlapper -name \*ovb.gz -print > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore.list ----------------------------------------END Wed Jan 28 11:10:48 2009 (0 seconds) ----------------------------------------START Wed Jan 28 11:10:48 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -c /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore.BUILDING -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -M 1024 -L /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore.list > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:50 2009 (2 seconds) ----------------------------------------START CONCURRENT Wed Jan 28 11:10:50 2009 sh /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/frgcorr.sh 1 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/0001.err 2>&1 ----------------------------------------END CONCURRENT Wed Jan 28 11:10:55 2009 (5 seconds) ----------------------------------------START Wed Jan 28 11:10:55 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cat-corrects -L /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/cat-corrects.frgcorrlist -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/bt.frgcorr > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/cat-corrects.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:55 2009 (0 seconds) ----------------------------------------START CONCURRENT Wed Jan 28 11:10:55 2009 sh /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/ovlcorr.sh 1 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/0001.err 2>&1 ----------------------------------------END CONCURRENT Wed Jan 28 11:10:58 2009 (3 seconds) ----------------------------------------START Wed Jan 28 11:10:58 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cat-erates -L /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/cat-erates.eratelist -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/bt.erates > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/cat-erates.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:58 2009 (0 seconds) ----------------------------------------START Wed Jan 28 11:10:58 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/overlapStore -u /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/bt.erates> /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./3-overlapcorrection/overlapStore-update-erates.err 2>&1 ----------------------------------------END Wed Jan 28 11:10:59 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 Wed Jan 28 11:10:59 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/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./4-unitigger/bt -I /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.ovlStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./4-unitigger/unitigger.err 2>&1 ----------------------------------------END Wed Jan 28 11:11:01 2009 (2 seconds) ----------------------------------------START Wed Jan 28 11:11:01 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -P /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt.partFile /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt.partitioned.err 2>&1 ----------------------------------------END Wed Jan 28 11:11:04 2009 (3 seconds) ----------------------------------------START CONCURRENT Wed Jan 28 11:11:04 2009 sh /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/consensus.sh 1 > /dev/null 2>&1 ----------------------------------------END CONCURRENT Wed Jan 28 11:12:12 2009 (68 seconds) ----------------------------------------START Wed Jan 28 11:12:12 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -j 1 -k 5 -r 5 -s 2 -S 0 -G -z -m 100 -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/bt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt_001.cgi > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/cgw.out 2>&1 ----------------------------------------END Wed Jan 28 11:12:25 2009 (13 seconds) ----------------------------------------START Wed Jan 28 11:12:26 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -a -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -E /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/gkp.distupdate.err /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/stat/scaffold_final.distupdate.dst /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/stat/contig_final.distupdate.dst > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./6-clonesize/cgw.distupdate.err 2>&1 ----------------------------------------END Wed Jan 28 11:12:26 2009 (0 seconds) ----------------------------------------START Wed Jan 28 11:12:26 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/cgw -j 1 -k 5 -r 5 -s 0 -S 0 -G -z -m 100 -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-0-CGW/bt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt_001.cgi > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-0-CGW/cgw.out 2>&1 ----------------------------------------END Wed Jan 28 11:12:37 2009 (11 seconds) Found 84 scaffolds in 7-1-ECR checkpoint number 4. ----------------------------------------START Wed Jan 28 11:12:38 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/extendClearRanges -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -n 4 -c bt -b 00 -e 84 -i 1 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-1-ECR/extendClearRanges-scaffold.00.err 2>&1 ----------------------------------------END Wed Jan 28 11:12:39 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:12:40 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 -G -z -m 100 -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-2-CGW/bt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt_001.cgi > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-2-CGW/cgw.out 2>&1 ----------------------------------------END Wed Jan 28 11:12:45 2009 (5 seconds) Found 19 scaffolds in 7-3-ECR checkpoint number 10. ----------------------------------------START Wed Jan 28 11:12:45 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/extendClearRanges -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -n 10 -c bt -b 00 -e 19 -i 2 > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-3-ECR/extendClearRanges-scaffold.00.err 2>&1 ----------------------------------------END Wed Jan 28 11:12:46 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:12:46 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/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-4-CGW/bt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./5-consensus/bt_001.cgi > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-4-CGW/cgw.out 2>&1 ----------------------------------------END Wed Jan 28 11:12:56 2009 (10 seconds) ----------------------------------------START Wed Jan 28 11:12:56 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/PartitionSDB -all -seqstore /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-CGW/bt.SeqStore -version 20 -fragsper 75000 -input /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-CGW/bt.cgw_contigs > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./8-consensus/partitionSDB.err 2>&1 ----------------------------------------END Wed Jan 28 11:12:57 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:12:57 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/gatekeeper -P /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./8-consensus/FragPartition.txt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./8-consensus/bt.partitioned.err 2>&1 ----------------------------------------END Wed Jan 28 11:12:58 2009 (1 seconds) ----------------------------------------START CONCURRENT Wed Jan 28 11:12:58 2009 sh /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./8-consensus/consensus.sh 1 > /dev/null 2>&1 ----------------------------------------END CONCURRENT Wed Jan 28 11:13:09 2009 (11 seconds) ----------------------------------------START Wed Jan 28 11:13:09 2009 cat /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-CGW/bt.cgw /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./8-consensus/bt.cns_contigs.*[0-9] /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-CGW/bt.cgw_scaffolds | /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/terminator -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -o /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/terminator.err 2>&1 ----------------------------------------END Wed Jan 28 11:13:10 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:13:10 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/asmOutputFasta -p /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.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 Wed Jan 28 11:13:11 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:13:11 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/dumpSingletons -g /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./bt.gkpStore -c /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./7-CGW/bt -n 20 -S > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.singleton.fasta 2> /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/dumpSingletons.err ----------------------------------------END Wed Jan 28 11:13:13 2009 (2 seconds) ----------------------------------------START Wed Jan 28 11:13:13 2009 /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/buildPosMap -o bt < /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.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 Wed Jan 28 11:13:14 2009 (1 seconds) ----------------------------------------START Wed Jan 28 11:13:14 2009 sort -k2n -T /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.sorted &&/fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 0 -max 3000 < /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.sorted > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.histogram1 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 3001 -max 10000 < /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.sorted > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.histogram2 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 10001 -max 1000000 < /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.sorted > /fs/szasmg3/bos_ taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.histogram3 && /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/fragmentDepth -min 1000001 < /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.posmap.frgscf.sorted > /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.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 Wed Jan 28 11:13:14 2009 (0 seconds) ----------------------------------------START Wed Jan 28 11:13:14 2009 /usr/bin/env perl /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/caqc.pl -euid -metrics /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator/bt.asm Cannot open /fs/szasmg3/bos_taurus/data/2009_0126_CA_test/./9-terminator//bt.frg at /fs/szdevel/dpuiu/SourceForge/wgs-5.2/Linux-amd64/bin/caqc.pl line 655. ----------------------------------------END Wed Jan 28 11:13:14 2009 (0 seconds) ERROR: Failed with signal INT (2) The Cleaner has arrived. Doing 'none'.