calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/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/LGG-TP/2283915/0.MutSigPreprocess.Finished/LGG-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LGG-TP/2283915/0.MutSigPreprocess.Finished/LGG-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LGG-TP/2283915/0.MutSigPreprocess.Finished/LGG-TP.maf
Started submitting scatter jobs at Thu Jan 10 14:40:47 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/285935/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-F2-7273-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-F2-7273-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-F2-7273-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-F2-7276-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-F2-7276-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-F2-7276-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6551-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6551-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6551-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6552-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6552-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6552-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6553-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6553-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6553-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6554-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6554-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6554-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6555-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6555-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6555-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6558-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6558-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6558-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FQ-6559-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FQ-6559-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FQ-6559-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5919-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5919-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5919-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5920-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5920-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5920-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5921-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5921-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5921-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5922-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5922-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5922-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5923-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5923-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5923-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5924-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5924-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5924-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-FZ-5926-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-FZ-5926-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FZ-5926-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-7918-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-7918-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-7918-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-7920-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-7920-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-7920-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-7924-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-7924-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-7924-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-7925-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-7925-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-7925-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-7926-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-7926-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-7926-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-8001-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-8001-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-8001-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-8002-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-8002-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-8002-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-8003-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-8003-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-8003-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-HZ-8005-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-HZ-8005-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-HZ-8005-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7645-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7645-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7645-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7649-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7649-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7649-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7886-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7886-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7886-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7887-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7887-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7887-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7889-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7889-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7889-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7890-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7890-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7890-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7891-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7891-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7891-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7893-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7893-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7893-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285935/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285935   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LGG-IB-7897-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LGG-IB-7897-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lgg/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LGG.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-IB-7897-01.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 14:41:22 2013 in 0.573644598325 minutes
calling:  bsub -E cd "/xchip/cga1/annotation" && 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_285935) -J gather_285935 -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/" "LGG-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LGG-TP/2283915/0.MutSigPreprocess.Finished/LGG-TP.maf" "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LGG-TP/2283915/0.MutSigPreprocess.Finished/LGG-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_285935) -J iteration_285935 -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 285935 --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
