calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1 -E cd "/xchip/tcga" && cd "/xchip/cga" -e prepare.err -oo prepare.out -K -P Firehose python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/OV-TP/2283999/0.MutSigPreprocess.Finished/OV-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/OV-TP/2283999/0.MutSigPreprocess.Finished/OV-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/OV-TP/2283999/0.MutSigPreprocess.Finished/OV-TP.maf
Started submitting scatter jobs at Thu Jan 10 14:40:52 2013
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1331-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1331-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-04-1331-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1332-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1332-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1332-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1336-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1336-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1336-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1337-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1337-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1337-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1338-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1338-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1338-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1342-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1342-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-04-1342-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1343-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1343-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1343-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1346-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1346-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1346-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1347-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1347-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1347-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1348-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1348-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1348-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1349-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1349-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1349-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1350-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1350-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1350-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1356-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1356-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-04-1356-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1357-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1357-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-04-1357-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1361-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1361-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1361-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1362-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1362-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1362-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1364-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1364-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1364-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1365-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1365-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1365-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1367-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1367-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-04-1367-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1514-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1514-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1514-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1517-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1517-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1517-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1525-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1525-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1525-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1530-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1530-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-04-1530-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-04-1542-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-04-1542-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-04-1542-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-0366-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-0366-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-09-0366-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-0369-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-0369-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-09-0369-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1659-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1659-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1659-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1661-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1661-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1661-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1662-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1662-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1662-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1665-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1665-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1665-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1666-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1666-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1666-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-1669-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-1669-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-09-1669-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2044-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2044-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2044-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2045-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2045-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2045-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000035/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2049-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2049-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2049-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000036/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2050-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2050-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2050-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000037/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2051-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2051-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2051-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000038/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2053-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2053-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2053-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000039/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-09-2056-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-09-2056-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-09-2056-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000040/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0926-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0926-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-10-0926-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000041/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0927-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0927-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-10-0927-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000042/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0928-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0928-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-10-0928-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000043/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0930-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0930-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-10-0930-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000044/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0931-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0931-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-10-0931-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000045/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0933-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0933-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-10-0933-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000046/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0934-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0934-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-10-0934-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000047/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0935-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0935-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-10-0935-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000048/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0937-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0937-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-10-0937-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000049/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-10-0938-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-10-0938-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-10-0938-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000050/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0714-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0714-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0714-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000051/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0717-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0717-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0717-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000052/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0720-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0720-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0720-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000053/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0723-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0723-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0723-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000054/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0724-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0724-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0724-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000055/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0726-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0726-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0726-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000056/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0727-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0727-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0727-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000057/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0730-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0730-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0730-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000058/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0751-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0751-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0751-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000059/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0755-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0755-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0755-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000060/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0760-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0760-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0760-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000061/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0761-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0761-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0761-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000062/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0762-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0762-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0762-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000063/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0765-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0765-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0765-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000064/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0791-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0791-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0791-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000065/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0792-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0792-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0792-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000066/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0793-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0793-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0793-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000067/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0795-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0795-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0795-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000068/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0800-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0800-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0800-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000069/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0804-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0804-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0804-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000070/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0807-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0807-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0807-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000071/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0883-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0883-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0883-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000072/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0884-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0884-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0884-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000073/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0885-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0885-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0885-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000074/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0886-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0886-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0886-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000075/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0887-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0887-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0887-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000076/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0889-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0889-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0889-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000077/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0890-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0890-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0890-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000078/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0891-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0891-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0891-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000079/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0893-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0893-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0893-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000080/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0894-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0894-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0894-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000081/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0897-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0897-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0897-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000082/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0899-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0899-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0899-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000083/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0900-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0900-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0900-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000084/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0903-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0903-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0903-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000085/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0904-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0904-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0904-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000086/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0905-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0905-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0905-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000087/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0906-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0906-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0906-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000088/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0910-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0910-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0910-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000089/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0911-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0911-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0911-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000090/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0912-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0912-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0912-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000091/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0913-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0913-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0913-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000092/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0916-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0916-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0916-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000093/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0919-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0919-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-0919-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000094/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0920-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0920-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0920-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000095/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0923-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0923-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-0923-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000096/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-0924-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-0924-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-0924-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000097/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1403-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1403-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1403-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000098/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1404-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1404-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1404-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000099/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1405-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1405-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1405-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000100/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1407-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1407-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-1407-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000101/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1408-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1408-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-13-1408-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000102/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1409-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1409-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1409-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000103/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1410-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1410-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1410-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000104/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1411-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1411-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1411-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000105/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1412-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1412-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1412-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000106/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1477-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1477-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1477-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000107/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1481-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1481-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1481-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000108/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1482-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1482-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1482-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000109/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1483-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1483-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1483-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000110/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1484-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1484-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1484-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000111/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1487-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1487-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1487-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000112/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1488-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1488-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1488-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000113/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1489-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1489-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1489-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000114/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1491-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1491-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1491-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000115/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1492-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1492-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1492-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000116/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1494-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1494-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1494-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000117/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1495-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1495-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1495-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000118/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1496-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1496-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1496-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000119/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1497-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1497-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1497-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000120/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1498-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1498-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1498-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000121/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1499-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1499-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1499-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000122/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1501-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1501-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1501-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000123/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1504-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1504-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1504-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000124/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1505-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1505-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1505-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000125/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1506-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1506-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1506-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000126/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1507-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1507-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1507-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000127/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1509-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1509-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-13-1509-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000128/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1510-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1510-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1510-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000129/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-1512-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-1512-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-1512-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000130/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-13-2060-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-13-2060-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-13-2060-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000131/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-20-0987-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-20-0987-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-20-0987-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000132/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-20-0990-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-20-0990-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-20-0990-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000133/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-20-0991-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-20-0991-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-20-0991-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000134/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1021-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1021-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1021-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000135/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1022-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1022-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1022-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000136/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1023-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1023-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-23-1023-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000137/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1024-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1024-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-23-1024-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000138/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1026-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1026-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-23-1026-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000139/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1027-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1027-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1027-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000140/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1028-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1028-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-23-1028-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000141/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1030-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1030-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1030-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000142/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1031-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1031-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1031-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000143/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1032-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1032-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1032-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000144/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1110-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1110-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1110-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000145/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1116-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1116-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1116-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000146/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1117-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1117-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1117-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000147/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1118-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1118-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1118-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000148/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1120-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1120-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-23-1120-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000149/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1122-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1122-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-1122-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000150/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1123-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1123-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1123-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000151/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-1124-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-1124-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-23-1124-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000152/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-2072-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-2072-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-2072-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000153/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-2077-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-2077-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-2077-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000154/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-2078-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-2078-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-2078-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000155/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-2079-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-2079-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-2079-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000156/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-23-2081-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-23-2081-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-23-2081-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000157/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0966-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0966-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-0966-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000158/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0968-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0968-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-0968-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000159/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0970-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0970-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-0970-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000160/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0975-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0975-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-0975-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000161/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0979-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0979-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-0979-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000162/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0980-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0980-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-0980-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000163/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-0982-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-0982-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-0982-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000164/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1103-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1103-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1103-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000165/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1104-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1104-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1104-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000166/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1105-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1105-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1105-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000167/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1413-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1413-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1413-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000168/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1416-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1416-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1416-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000169/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1417-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1417-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1417-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000170/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1418-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1418-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1418-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000171/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1419-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1419-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1419-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000172/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1422-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1422-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1422-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000173/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1423-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1423-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1423-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000174/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1424-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1424-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1424-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000175/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1425-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1425-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1425-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000176/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1426-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1426-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1426-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000177/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1427-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1427-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1427-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000178/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1428-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1428-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1428-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000179/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1431-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1431-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1431-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000180/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1434-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1434-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1434-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000181/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1435-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1435-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1435-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000182/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1436-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1436-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1436-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000183/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1463-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1463-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1463-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000184/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1464-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1464-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1464-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000185/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1466-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1466-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1466-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000186/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1469-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1469-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1469-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000187/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1470-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1470-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1470-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000188/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1471-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1471-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1471-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000189/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1474-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1474-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1474-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000190/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1544-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1544-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1544-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000191/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1545-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1545-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1545-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000192/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1548-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1548-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1548-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000193/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1549-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1549-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1549-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000194/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1551-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1551-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1551-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000195/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1552-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1552-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1552-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000196/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1553-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1553-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1553-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000197/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1555-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1555-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1555-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000198/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1556-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1556-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1556-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000199/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1557-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1557-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1557-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000200/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1558-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1558-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1558-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000201/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1560-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1560-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1560-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000202/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1562-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1562-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1562-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000203/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1563-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1563-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1563-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000204/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1564-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1564-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1564-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000205/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1565-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1565-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1565-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000206/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1567-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1567-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1567-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000207/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1603-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1603-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-1603-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000208/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1604-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1604-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1604-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000209/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1614-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1614-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-24-1614-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000210/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-1616-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-1616-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-24-1616-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000211/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2019-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2019-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2019-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000212/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2024-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2024-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2024-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000213/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2030-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2030-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2030-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000214/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2035-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2035-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2035-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000215/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2038-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2038-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2038-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000216/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2254-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2254-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2254-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000217/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2260-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2260-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2260-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000218/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2261-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2261-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2261-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000219/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2262-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2262-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2262-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000220/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2267-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2267-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2267-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000221/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2271-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2271-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2271-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000222/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2280-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2280-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2280-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000223/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2281-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2281-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2281-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000224/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2288-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2288-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2288-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000225/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2289-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2289-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2289-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000226 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000226/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2290-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2290-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2290-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000227 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000227/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2293-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2293-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2293-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000228 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000228/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-24-2298-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-24-2298-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-24-2298-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000229 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000229/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1313-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1313-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1313-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000230 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000230/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1315-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1315-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-25-1315-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000231 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000231/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1316-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1316-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-25-1316-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000232 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000232/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1317-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1317-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1317-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000233 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000233/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1318-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1318-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1318-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000234 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000234/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1319-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1319-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1319-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000235 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000235/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1320-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1320-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1320-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000236 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000236/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1321-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1321-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1321-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000237 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000237/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1322-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1322-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_OV.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-25-1322-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000238 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000238/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1324-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1324-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1324-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000239 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000239/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1326-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1326-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1326-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000240 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000240/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1328-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1328-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1328-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000241 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000241/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1329-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1329-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-1329-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000242 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000242/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1623-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1623-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1623-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000243 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000243/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1625-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1625-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1625-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000244 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000244/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1626-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1626-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1626-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000245 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000245/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1627-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1627-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1627-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000246 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000246/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1628-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1628-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1628-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000247 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000247/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1630-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1630-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1630-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000248 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000248/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1631-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1631-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1631-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000249 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000249/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1632-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1632-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1632-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000250 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000250/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1633-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1633-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1633-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000251 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000251/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1634-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1634-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1634-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000252 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000252/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-1635-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-1635-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-25-1635-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000253 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000253/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2042-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2042-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2042-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000254 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000254/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2391-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2391-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2391-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000255 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000255/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2392-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2392-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2392-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000256 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000256/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2393-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2393-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2393-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000257 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000257/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2396-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2396-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2396-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000258 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000258/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2398-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2398-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2398-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000259 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000259/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2399-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2399-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2399-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000260 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000260/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2400-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2400-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2400-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000261 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000261/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2401-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2401-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2401-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000262 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000262/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2404-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2404-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2404-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000263 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000263/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2408-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2408-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2408-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000264 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000264/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-25-2409-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-25-2409-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-25-2409-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000265 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000265/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-29-2427-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-29-2427-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-29-2427-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000266 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000266/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-30-1853-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-30-1853-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-30-1853-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000267 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000267/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-30-1862-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-30-1862-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-30-1862-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000268 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000268/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-30-1891-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-30-1891-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-30-1891-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000269 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000269/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-31-1950-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-31-1950-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-31-1950-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000270 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000270/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-31-1953-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-31-1953-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-31-1953-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000271 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000271/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-31-1959-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-31-1959-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-31-1959-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000272 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000272/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1568-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1568-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1568-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000273 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000273/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1569-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1569-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1569-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000274 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000274/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1570-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1570-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1570-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000275 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000275/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1571-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1571-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1571-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000276 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000276/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1574-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1574-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1574-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000277 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000277/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1575-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1575-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1575-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000278 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000278/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1576-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1576-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1576-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000279 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000279/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1577-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1577-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1577-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000280 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000280/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1578-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1578-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1578-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000281 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000281/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-36-1580-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-36-1580-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-36-1580-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000282 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000282/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-57-1582-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-57-1582-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-57-1582-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000283 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000283/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-57-1583-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-57-1583-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-57-1583-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000284 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000284/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-57-1584-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-57-1584-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_OV.SOLiD_DNA.Level_2.2.5.0/TCGA-57-1584-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000285 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000285/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-57-1993-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-57-1993-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-57-1993-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000286 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000286/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2348-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2348-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2348-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000287 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000287/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2350-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2350-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2350-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000288 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000288/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2351-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2351-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2351-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000289 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000289/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2352-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2352-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2352-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000290 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000290/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2354-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2354-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2354-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000291 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000291/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2355-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2355-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2355-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000292 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000292/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-59-2363-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-59-2363-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-59-2363-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000293 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000293/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-1728-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-1728-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-1728-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000294 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000294/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-1736-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-1736-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-1736-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000295 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000295/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-1919-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-1919-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-1919-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000296 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000296/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-1995-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-1995-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-1995-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000297 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000297/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-1998-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-1998-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-1998-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000298 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000298/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2000-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2000-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2000-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000299 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000299/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2002-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2002-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2002-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000300 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000300/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2003-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2003-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2003-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000301 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000301/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2008-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2008-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000302 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000302/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2009-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2009-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2009-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000303 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000303/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2012-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2012-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2012-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000304 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000304/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2016-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2016-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000305 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000305/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2088-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2088-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2088-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000306 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000306/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2092-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2092-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2092-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000307 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000307/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2094-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2094-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2094-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000308 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000308/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2095-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2095-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2095-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000309 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000309/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2097-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2097-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2097-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000310 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000310/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2101-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2101-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2101-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000311 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000311/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2102-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2102-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2102-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000312 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000312/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2104-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2104-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2104-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000313 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000313/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2109-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2109-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2109-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000314 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000314/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2110-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2110-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2110-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000315 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000315/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2111-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2111-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2111-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000316 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285976/iteration1/scatter.0000000316/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285976   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "OV-61-2113-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "OV-61-2113-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ov/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_OV.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-61-2113-01.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 14:45:56 2013 in 5.07089176575 minutes
calling:  bsub -E cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e scatter-gather.err.txt -o scatter-gather.out.txt -w ended(scatter_285976) -J gather_285976 -P Firehose -R rusage[mem=12] -sp 65   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ fh_MutSigCoverageGather   "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/" "OV-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/OV-TP/2283999/0.MutSigPreprocess.Finished/OV-TP.maf" "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/OV-TP/2283999/0.MutSigPreprocess.Finished/OV-TP.patients.txt"

calling:  bsub -E cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e iterator.err.txt -o iterator.out.txt -w ended(gather_285976) -J iteration_285976 -P Firehose -sp 65   /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 285976 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
Path iteration1 exists:  True
