calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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/GBM-TP/2283735/0.MutSigPreprocess.Finished/GBM-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM-TP/2283735/0.MutSigPreprocess.Finished/GBM-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM-TP/2283735/0.MutSigPreprocess.Finished/GBM-TP.maf
Started submitting scatter jobs at Thu Jan 10 14:40:51 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/285883/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-0003-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-0003-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0003-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-0033-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-0033-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0033-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-0047-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-0047-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0047-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-0055-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-0055-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0055-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-2470-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-2470-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2470-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-2483-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-2483-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2483-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-2485-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-2485-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2485-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-02-2486-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-02-2486-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2486-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0119-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0119-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0119-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0122-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0122-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0122-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0124-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0124-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0124-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0125-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0125-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0125-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0126-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0126-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0126-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0128-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0128-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0128-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0129-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0129-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0129-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0130-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0130-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0130-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0132-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0132-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0132-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0137-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0137-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0137-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0139-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0139-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0139-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0140-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0140-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0140-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0141-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0141-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0141-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0142-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0142-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0142-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0145-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0145-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0145-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0151-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0151-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0151-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0152-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0152-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0152-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0154-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0154-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0154-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0155-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0155-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0155-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0157-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0157-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0157-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0158-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0158-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0158-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0165-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0165-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0165-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0166-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0166-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0166-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0167-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0167-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0167-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0168-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0168-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0168-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0169-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0169-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0169-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0171-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0171-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0171-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0173-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0173-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0173-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0174-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0174-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0174-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0178-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0178-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0178-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0184-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0184-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0184-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0185-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0185-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0185-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0188-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0188-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0188-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0189-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0189-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0189-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0190-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0190-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0190-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0192-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0192-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0192-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0195-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0195-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0195-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0209-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0209-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0209-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0210-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0210-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0210-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0211-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0211-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0211-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0213-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0213-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0213-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0214-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0214-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0214-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0216-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0216-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0216-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0219-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0219-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0219-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0221-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0221-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0221-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0237-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0237-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0237-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0238-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0238-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0238-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0240-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0240-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0240-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0241-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0241-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0241-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0644-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0644-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0644-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0645-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0645-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0645-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0646-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0646-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0646-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0648-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0648-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0648-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0649-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0649-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0649-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0650-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0650-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0650-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0686-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0686-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0686-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0743-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0743-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0743-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0744-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0744-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0744-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0745-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0745-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0745-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0747-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0747-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0747-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0749-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0749-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0749-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0750-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0750-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0750-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0875-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0875-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0875-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0876-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0876-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0876-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0877-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0877-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0877-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0878-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0878-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0878-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0879-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0879-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0879-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0881-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0881-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0881-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0882-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0882-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0882-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-0939-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-0939-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0939-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-1804-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-1804-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-1804-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-1806-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-1806-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-1806-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2557-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2557-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2557-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2558-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2558-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2558-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2559-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2559-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2559-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2561-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2561-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2561-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2562-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2562-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2562-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2563-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2563-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2563-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2564-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2564-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2564-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2565-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2565-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2565-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2567-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2567-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2567-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2569-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2569-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2569-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-2570-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-2570-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2570-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5408-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5408-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5408-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5410-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5410-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5410-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5411-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5411-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5411-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5412-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5412-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5412-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5413-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5413-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5413-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5414-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5414-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5414-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5415-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5415-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5415-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5417-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5417-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5417-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5418-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5418-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5418-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5856-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5856-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5856-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5858-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5858-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5858-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-5859-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-5859-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5859-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6388-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6388-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6388-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6389-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6389-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6389-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6390-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6390-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6390-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6391-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6391-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6391-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6693-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6693-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6693-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6694-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6694-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6694-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6695-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6695-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6695-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6697-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6697-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6697-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6698-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6698-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6698-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6699-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6699-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6699-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6700-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6700-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6700-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-06-6701-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-06-6701-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6701-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-08-0386-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-08-0386-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-08-0386-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0615-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0615-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0615-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0616-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0616-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0616-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0618-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0618-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0618-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0619-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0619-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0619-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0688-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0688-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0688-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0692-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0692-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0692-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-0821-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-0821-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0821-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-1597-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-1597-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-1597-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-3649-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-3649-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3649-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-3650-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-3650-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3650-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-3652-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-3652-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3652-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-3653-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-3653-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3653-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-5295-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-5295-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5295-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-5299-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-5299-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5299-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-12-5301-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-12-5301-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5301-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0740-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0740-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0740-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0781-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0781-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0781-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0786-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0786-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0786-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0787-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0787-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0787-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0789-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0789-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0789-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0790-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0790-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0790-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0813-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0813-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0813-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0817-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0817-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0817-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0862-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0862-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0862-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-0871-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-0871-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0871-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1034-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1034-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1034-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1043-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1043-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1043-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1395-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1395-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1395-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1450-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1450-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1450-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1456-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1456-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1456-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1823-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1823-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1823-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1825-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1825-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1825-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-1829-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-1829-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1829-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-2554-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-2554-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-2554-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-3476-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-3476-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-3476-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-14-4157-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-14-4157-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-4157-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-15-0742-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-15-0742-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-15-0742-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-15-1444-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-15-1444-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-15-1444-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-16-0846-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-16-0846-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-0846-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-16-0861-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-16-0861-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-0861-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-16-1045-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-16-1045-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-1045-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-16-1048-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-16-1048-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-1048-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-1390-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-1390-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-1390-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-1790-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-1790-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-1790-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2619-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2619-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2619-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2620-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2620-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2620-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2623-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2623-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2623-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2624-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2624-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2624-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2625-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2625-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2625-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2629-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2629-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2629-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-2631-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-2631-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2631-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-4068-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-4068-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-4068-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5947-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5947-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5947-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5950-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5950-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5950-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5951-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5951-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5951-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5952-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5952-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5952-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5953-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5953-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5953-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5954-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5954-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5954-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5955-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5955-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5955-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5958-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5958-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5958-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5959-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5959-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5959-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-19-5960-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-19-5960-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5960-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-1439-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-1439-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-1439-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-1442-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-1442-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-1442-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5132-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5132-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5132-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5133-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5133-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5133-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5134-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5134-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5134-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5135-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5135-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5135-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5136-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5136-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5136-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-5139-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-5139-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5139-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-6173-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-6173-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-6173-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-26-6174-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-26-6174-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-6174-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1830-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1830-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1830-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1831-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1831-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1831-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1832-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1832-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1832-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1833-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1833-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1833-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1834-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1834-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1834-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1835-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1835-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1835-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1836-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1836-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1836-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1837-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1837-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1837-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-1838-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-1838-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1838-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2518-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2518-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2518-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2519-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2519-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2519-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2521-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2521-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2521-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2523-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2523-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2523-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2524-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2524-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2524-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2526-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2526-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2526-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2527-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2527-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2527-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-27-2528-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-27-2528-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2528-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-1747-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-1747-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-1747-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-1753-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-1753-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-1753-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2499-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2499-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2499-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2501-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2501-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2501-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2502-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2502-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2502-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2509-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2509-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2509-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2510-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2510-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2510-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2513-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2513-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2513-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-2514-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-2514-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2514-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5204-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5204-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5204-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5207-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5207-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5207-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5208-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5208-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5208-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5209-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5209-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5209-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5211-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5211-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5211-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5213-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5213-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5213-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5214-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5214-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5214-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5215-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5215-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5215-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5216-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5216-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5216-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5218-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5218-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5218-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5219-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5219-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5219-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000226 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-5220-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-5220-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5220-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000227 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-28-6450-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-28-6450-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-6450-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000228 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1970-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1970-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1970-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000229 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1977-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1977-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1977-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000230 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1979-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1979-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1979-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000231 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1980-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1980-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1980-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000232 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1982-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1982-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1982-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000233 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1986-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1986-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1986-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000234 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-1991-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-1991-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1991-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000235 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2491-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2491-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2491-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000236 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2494-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2494-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2494-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000237 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2495-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2495-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2495-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000238 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2498-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2498-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2498-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000239 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2615-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2615-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2615-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000240 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2632-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2632-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2632-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000241 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2634-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2634-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2634-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000242 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-2638-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-2638-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2638-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000243 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4208-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4208-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4208-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000244 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4209-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4209-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4209-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000245 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4210-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4210-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4210-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000246 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4211-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4211-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4211-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000247 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4213-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4213-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4213-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000248 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-4719-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-4719-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4719-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000249 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-32-5222-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-32-5222-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-5222-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000250 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-2571-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-2571-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2571-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000251 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-2572-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-2572-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2572-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000252 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-2573-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-2573-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2573-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000253 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-2575-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-2575-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2575-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000254 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-3392-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-3392-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3392-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000255 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-3393-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-3393-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3393-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000256 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-3915-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-3915-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3915-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000257 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-4097-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-4097-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-4097-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000258 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-5651-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-5651-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-5651-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000259 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-41-6646-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-41-6646-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-6646-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000260 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-74-6573-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-74-6573-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6573-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000261 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-74-6575-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-74-6575-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6575-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000262 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-74-6577-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-74-6577-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6577-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000263 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-74-6578-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-74-6578-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6578-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000264 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-74-6584-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-74-6584-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6584-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000265 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4925-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4925-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4925-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000266 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4926-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4926-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4926-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000267 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4927-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4927-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4927-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000268 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4928-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4928-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4928-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000269 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4929-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4929-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4929-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000270 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4931-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4931-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4931-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000271 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4932-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4932-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4932-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000272 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4934-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4934-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4934-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000273 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-4935-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-4935-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4935-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000274 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6191-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6191-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6191-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000275 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6192-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6192-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6192-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000276 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6193-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6193-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6193-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000277 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6280-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6280-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6280-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000278 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6282-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6282-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6282-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000279 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6283-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6283-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6283-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000280 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6285-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6285-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6285-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000281 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6286-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6286-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6286-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000282 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6656-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6656-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6656-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000283 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6657-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6657-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6657-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000284 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6660-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6660-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6660-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000285 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6661-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6661-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6661-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000286 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6662-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6662-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6662-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000287 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6663-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6663-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6663-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000288 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-76-6664-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-76-6664-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6664-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000289 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-81-5910-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-81-5910-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-81-5910-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000290 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-81-5911-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-81-5911-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-81-5911-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/iteration1/scatter.0000000291 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285883/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_285883   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "GBM-87-5896-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "GBM-87-5896-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-87-5896-01.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 14:45:33 2013 in 4.68963198264 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_285883) -J gather_285883 -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/" "GBM-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM-TP/2283735/0.MutSigPreprocess.Finished/GBM-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/GBM-TP/2283735/0.MutSigPreprocess.Finished/GBM-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_285883) -J iteration_285883 -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 285883 --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
