calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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/READ-TP/2284074/0.MutSigPreprocess.Finished/READ-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ-TP/2284074/0.MutSigPreprocess.Finished/READ-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ-TP/2284074/0.MutSigPreprocess.Finished/READ-TP.maf
Started submitting scatter jobs at Thu Jan 10 19:13:42 2013
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AF-2689-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2689-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AF-2689-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AF-2691-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2691-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AF-2691-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AF-2692-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2692-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AF-2692-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AF-3400-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-3400-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AF-3400-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AF-3913-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-3913-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AF-3913-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3574-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3574-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3574-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3575-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3575-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3575-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3578-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3578-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3578-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3580-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3580-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3580-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3581-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3581-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3581-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3582-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3582-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3582-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3583-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3583-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3583-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3584-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3584-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3584-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3586-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3586-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3586-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3587-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3587-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3587-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3593-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3593-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3593-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3594-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3594-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3594-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3598-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3598-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3598-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3599-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3599-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3599-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3600-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3600-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3600-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3601-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3601-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3601-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3602-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3602-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3602-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3605-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3605-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3605-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3608-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3608-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3608-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3609-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3609-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3609-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3611-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3611-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3611-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3612-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3612-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-3612-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3726-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3726-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3726-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3727-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3727-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3727-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3878-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3878-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3878-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3881-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3881-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3881-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3882-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3882-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3882-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3883-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3883-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3883-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3887-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3887-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3887-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3890-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3890-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3890-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3892-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3892-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3892-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3893-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3893-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3893-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3894-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3894-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3894-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3896-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3896-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3896-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3898-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3898-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3898-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3901-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3901-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3901-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3902-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3902-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3902-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3909-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3909-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3909-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-3999-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3999-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3999-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-4001-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4001-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4001-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-4005-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4005-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4005-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-4007-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4007-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4007-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-4008-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4008-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-4015-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4015-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4015-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A002-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A002-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A002-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A002-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A008-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A008-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A00C-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00C-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A00C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A00H-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A00H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A00Y-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A00Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A011-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A011-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A011-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A011-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A014-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A014-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A014-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A014-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A015-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A015-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A015-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A016-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A016-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A01L-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01L-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.2.4.0/TCGA-AG-A01L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A01W-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A01Y-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A020-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A020-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A020-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A025-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A025-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A025-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A026-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A026-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A026-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A02G-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02G-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A02N-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A02X-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A032-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A032-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A032-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286654/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_286654   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "READ-AG-A036-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A036-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A036-01.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 19:14:49 2013 in 1.10403839747 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_286654) -J gather_286654 -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/" "READ-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ-TP/2284074/0.MutSigPreprocess.Finished/READ-TP.maf" "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ-TP/2284074/0.MutSigPreprocess.Finished/READ-TP.patients.txt"

calling:  bsub -E cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e iterator.err.txt -o iterator.out.txt -w ended(gather_286654) -J iteration_286654 -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 286654 --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
