calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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/COAD/1798094/0.MutSigPreprocess.Finished/COAD.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1798094/0.MutSigPreprocess.Finished/COAD.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1798094/0.MutSigPreprocess.Finished/COAD.maf
Started submitting scatter jobs at Wed Oct 10 10:54:04 2012
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2670" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2670.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2670-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2672" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2672.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2672-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2674" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2674.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2674-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2676" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2676.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2676-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2677" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2677.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2677-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2678" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2678.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2678-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-2683" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-2683.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2683-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-3807" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-3807.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3807-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-3808" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-3808.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3808-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-A6-3810" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-A6-3810.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3810-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3514" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3514.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3514-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3516" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3516.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3516-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3517" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3517.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3517-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3518" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3518.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3518-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3519" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3519.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3519-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3520" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3520.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3520-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3521" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3521.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3521-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3522" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3522.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3522-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3524" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3524.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3524-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3525" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3525.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3525-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3526" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3526.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3526-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3527" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3527.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3527-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3529" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3529.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3529-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3530" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3530.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3530-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3531" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3531.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3531-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3532" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3532.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3532-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3534" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3534.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3534-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3538" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3538.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3538-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3542" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3542.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3542-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3543" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3543.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3543-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3544" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3544.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3544-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3548" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3548.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3548-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3549" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3549.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3549-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3552" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3552.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3552-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3553" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3553.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3553-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3554" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3554.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3554-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3555" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3555.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3555-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3556" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3556.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3556-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3558" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3558.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3558-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3560" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3560.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3560-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3561" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3561.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3561-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3562" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3562.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3562-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3664" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3664.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3664-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3666" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3666.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3666-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3667" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3667.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3667-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3672" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3672.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3672-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3673" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3673.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3673-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3678" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3678.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3678-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3679" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3679.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3679-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3680" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3680.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3680-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3681" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3681.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3681-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3684" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3684.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3684-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3685" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3685.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3685-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3688" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3688.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3688-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3692" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3692.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3692-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3693" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3693.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3693-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3695" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3695.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3695-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3696" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3696.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3696-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3710" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3710.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3710-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3715" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3715.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3715-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3811" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3811.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3811-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3812" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3812.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3812-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3814" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3814.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3814-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3818" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3818.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3818-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3819" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3819.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3819-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3821" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3821.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3821-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3831" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3831.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3831-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3833" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3833.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3833-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3837" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3837.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3837-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3842" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3842.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3842-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3844" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3844.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3844-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3845" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3845.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3845-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3846" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3846.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3846-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3848" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3848.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3848-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3850" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3850.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3850-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3851" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3851.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3851-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3852" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3852.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3852-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3854" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3854.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3854-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3855" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3855.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3855-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3856" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3856.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3856-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3858" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3858.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3858-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3860" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3860.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3860-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3864" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3864.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3864-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3866" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3866.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3866-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3867" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3867.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3867-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3869" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3869.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3869-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3870" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3870.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3870-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3872" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3872.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3872-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3875" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3875.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3875-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3877" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3877.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3877-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3930" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3930.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3930-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3939" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3939.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3939-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3941" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3941.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3941-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3947" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3947.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3947-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3949" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3949.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3949-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3952" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3952.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3952-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3955" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3955.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3955-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3956" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3956.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3956-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3966" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3966.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3966-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3971" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3971.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3971-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3972" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3972.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3972-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3973" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3973.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3973-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3975" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3975.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3975-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3976" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3976.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3976-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3977" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3977.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3977-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3979" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3979.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3979-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3980" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3980.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3980-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3982" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3982.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3982-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3984" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3984.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3984-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3986" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3986.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3986-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3989" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3989.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3989-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-3994" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-3994.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3994-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A004" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A004.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A004-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00A" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00D" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00E" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00E.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00F" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00J" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00K" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00L" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00N" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A00N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00O" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A00O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00Q" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00R" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00U" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00W" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A00Z" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A00Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A010" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A010.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A010-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A017" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A017.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A017-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01D" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01F" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01G" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01I" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01K" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01P" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01Q" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01R" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01S" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01S.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01T" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01V" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01X" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A01Z" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A01Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A022" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A022.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A022-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A024" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A024.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A024-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A029" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A029.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A029-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02F" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02H" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02J" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02O" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02W" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A02Y" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A02Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A03F" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A03F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A03F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AA-A03J" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AA-A03J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A03J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AY-4070" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AY-4070.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AY-4070-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181732/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_181732   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "COAD-AY-4071" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "COAD-AY-4071.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AY-4071-01.wig.txt"

Finished submitting scatter jobs at Wed Oct 10 10:57:34 2012 in 3.50572059949 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_181732) -J gather_181732 -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/" "COAD" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1798094/0.MutSigPreprocess.Finished/COAD.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/COAD/1798094/0.MutSigPreprocess.Finished/COAD.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_181732) -J iteration_181732 -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 181732 --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
