calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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/SKCM-TM/2284096/0.MutSigPreprocess.Finished/SKCM-TM.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/SKCM-TM/2284096/0.MutSigPreprocess.Finished/SKCM-TM.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/SKCM-TM/2284096/0.MutSigPreprocess.Finished/SKCM-TM.maf
Started submitting scatter jobs at Thu Jan 10 19:35:38 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/286698/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q1-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q1-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q1-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q4-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q4-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q4-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q6-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q6-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q6-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1Q9-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1Q9-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1Q9-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1QA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1QA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1QA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A1QB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A1QB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A1QB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2J6-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2J6-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2J6-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2J7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2J7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2J7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2J8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2J8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2J8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2J9-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2J9-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2J9-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JG-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JG-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JG-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JK-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JK-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JK-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JL-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JL-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JL-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JN-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JN-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JN-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JO-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JO-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JO-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A2JP-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A2JP-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A2JP-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3BZ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3BZ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3BZ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3C1-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3C1-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3C1-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3C3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3C3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3C3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3C6-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3C6-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3C6-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3C7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3C7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3C7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3C8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3C8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3C8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3CB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3CB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3CB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/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_286698   java -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 "SKCM-D3-A3CC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3CC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3CC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000035/*; 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_286698   java -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 "SKCM-D3-A3CE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3CE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3CE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000036/*; 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_286698   java -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 "SKCM-D3-A3CF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3CF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3CF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000037/*; 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_286698   java -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 "SKCM-D3-A3ML-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3ML-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3ML-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000038/*; 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_286698   java -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 "SKCM-D3-A3MO-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3MO-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3MO-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000039/*; 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_286698   java -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 "SKCM-D3-A3MR-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3MR-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3MR-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000040/*; 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_286698   java -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 "SKCM-D3-A3MU-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3MU-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3MU-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000041/*; 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_286698   java -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 "SKCM-D3-A3MV-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D3-A3MV-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D3-A3MV-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000042/*; 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_286698   java -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 "SKCM-D9-A148-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D9-A148-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D9-A148-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000043/*; 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_286698   java -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 "SKCM-D9-A149-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D9-A149-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D9-A149-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000044/*; 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_286698   java -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 "SKCM-D9-A1JW-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D9-A1JW-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D9-A1JW-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000045/*; 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_286698   java -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 "SKCM-D9-A1JX-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-D9-A1JX-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D9-A1JX-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000046/*; 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_286698   java -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 "SKCM-DA-A1HV-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1HV-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1HV-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000047/*; 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_286698   java -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 "SKCM-DA-A1HW-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1HW-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1HW-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000048/*; 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_286698   java -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 "SKCM-DA-A1HY-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1HY-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1HY-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000049/*; 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_286698   java -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 "SKCM-DA-A1I0-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I0-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I0-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000050/*; 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_286698   java -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 "SKCM-DA-A1I1-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I1-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I1-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000051/*; 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_286698   java -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 "SKCM-DA-A1I2-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I2-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I2-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000052/*; 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_286698   java -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 "SKCM-DA-A1I4-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I4-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I4-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000053/*; 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_286698   java -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 "SKCM-DA-A1I5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000054/*; 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_286698   java -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 "SKCM-DA-A1I7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000055/*; 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_286698   java -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 "SKCM-DA-A1I8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1I8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1I8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000056/*; 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_286698   java -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 "SKCM-DA-A1IA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1IA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1IA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000057/*; 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_286698   java -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 "SKCM-DA-A1IB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1IB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1IB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000058/*; 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_286698   java -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 "SKCM-DA-A1IC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A1IC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A1IC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000059/*; 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_286698   java -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 "SKCM-DA-A3F2-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A3F2-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A3F2-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000060/*; 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_286698   java -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 "SKCM-DA-A3F3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A3F3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A3F3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000061/*; 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_286698   java -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 "SKCM-DA-A3F5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A3F5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A3F5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000062/*; 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_286698   java -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 "SKCM-DA-A3F8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-DA-A3F8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-DA-A3F8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000063/*; 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_286698   java -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 "SKCM-EE-A17X-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A17X-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A17X-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000064/*; 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_286698   java -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 "SKCM-EE-A17Y-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A17Y-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A17Y-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000065/*; 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_286698   java -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 "SKCM-EE-A17Z-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A17Z-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A17Z-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000066/*; 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_286698   java -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 "SKCM-EE-A180-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A180-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A180-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000067/*; 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_286698   java -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 "SKCM-EE-A181-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A181-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A181-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000068/*; 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_286698   java -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 "SKCM-EE-A182-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A182-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A182-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000069/*; 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_286698   java -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 "SKCM-EE-A183-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A183-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A183-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000070/*; 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_286698   java -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 "SKCM-EE-A184-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A184-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A184-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000071/*; 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_286698   java -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 "SKCM-EE-A185-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A185-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A185-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000072/*; 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_286698   java -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 "SKCM-EE-A20B-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A20B-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A20B-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000073/*; 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_286698   java -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 "SKCM-EE-A20C-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A20C-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A20C-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000074/*; 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_286698   java -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 "SKCM-EE-A20F-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A20F-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A20F-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000075/*; 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_286698   java -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 "SKCM-EE-A20H-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A20H-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A20H-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000076/*; 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_286698   java -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 "SKCM-EE-A20I-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A20I-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A20I-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000077/*; 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_286698   java -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 "SKCM-EE-A29A-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29A-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29A-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000078/*; 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_286698   java -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 "SKCM-EE-A29B-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29B-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29B-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000079/*; 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_286698   java -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 "SKCM-EE-A29C-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29C-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29C-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000080/*; 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_286698   java -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 "SKCM-EE-A29D-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29D-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29D-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000081/*; 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_286698   java -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 "SKCM-EE-A29E-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29E-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29E-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000082/*; 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_286698   java -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 "SKCM-EE-A29G-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29G-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29G-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000083/*; 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_286698   java -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 "SKCM-EE-A29H-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29H-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29H-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000084/*; 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_286698   java -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 "SKCM-EE-A29L-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29L-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29L-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000085/*; 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_286698   java -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 "SKCM-EE-A29M-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29M-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29M-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000086/*; 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_286698   java -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 "SKCM-EE-A29N-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29N-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29N-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000087/*; 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_286698   java -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 "SKCM-EE-A29P-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29P-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29P-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000088/*; 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_286698   java -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 "SKCM-EE-A29Q-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29Q-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29Q-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000089/*; 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_286698   java -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 "SKCM-EE-A29R-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29R-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29R-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000090/*; 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_286698   java -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 "SKCM-EE-A29S-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29S-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29S-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000091/*; 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_286698   java -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 "SKCM-EE-A29T-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29T-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29T-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000092/*; 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_286698   java -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 "SKCM-EE-A29V-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29V-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29V-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000093/*; 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_286698   java -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 "SKCM-EE-A29W-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29W-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29W-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000094/*; 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_286698   java -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 "SKCM-EE-A29X-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A29X-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A29X-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000095/*; 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_286698   java -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 "SKCM-EE-A2A0-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2A0-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2A0-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000096/*; 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_286698   java -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 "SKCM-EE-A2A1-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2A1-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2A1-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000097/*; 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_286698   java -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 "SKCM-EE-A2A2-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2A2-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2A2-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000098/*; 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_286698   java -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 "SKCM-EE-A2A5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2A5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2A5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000099/*; 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_286698   java -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 "SKCM-EE-A2A6-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2A6-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2A6-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000100/*; 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_286698   java -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 "SKCM-EE-A2GB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000101/*; 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_286698   java -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 "SKCM-EE-A2GC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000102/*; 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_286698   java -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 "SKCM-EE-A2GD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000103/*; 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_286698   java -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 "SKCM-EE-A2GE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000104/*; 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_286698   java -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 "SKCM-EE-A2GH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000105/*; 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_286698   java -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 "SKCM-EE-A2GI-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GI-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GI-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000106/*; 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_286698   java -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 "SKCM-EE-A2GJ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GJ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GJ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000107/*; 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_286698   java -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 "SKCM-EE-A2GK-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GK-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GK-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000108/*; 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_286698   java -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 "SKCM-EE-A2GL-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GL-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GL-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000109/*; 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_286698   java -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 "SKCM-EE-A2GM-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GM-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GM-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000110/*; 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_286698   java -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 "SKCM-EE-A2GN-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GN-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GN-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000111/*; 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_286698   java -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 "SKCM-EE-A2GO-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GO-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GO-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000112/*; 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_286698   java -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 "SKCM-EE-A2GP-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GP-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GP-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000113/*; 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_286698   java -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 "SKCM-EE-A2GR-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GR-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GR-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000114/*; 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_286698   java -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 "SKCM-EE-A2GS-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GS-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GS-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000115/*; 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_286698   java -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 "SKCM-EE-A2GT-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GT-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GT-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000116/*; 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_286698   java -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 "SKCM-EE-A2GU-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2GU-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2GU-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000117/*; 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_286698   java -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 "SKCM-EE-A2M5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2M5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2M5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000118/*; 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_286698   java -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 "SKCM-EE-A2M6-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2M6-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2M6-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000119/*; 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_286698   java -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 "SKCM-EE-A2M7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2M7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2M7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000120/*; 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_286698   java -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 "SKCM-EE-A2M8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2M8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2M8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000121/*; 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_286698   java -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 "SKCM-EE-A2MC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000122/*; 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_286698   java -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 "SKCM-EE-A2MD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000123/*; 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_286698   java -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 "SKCM-EE-A2ME-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2ME-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2ME-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000124/*; 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_286698   java -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 "SKCM-EE-A2MF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000125/*; 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_286698   java -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 "SKCM-EE-A2MG-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MG-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MG-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000126/*; 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_286698   java -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 "SKCM-EE-A2MH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000127/*; 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_286698   java -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 "SKCM-EE-A2MI-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MI-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MI-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000128/*; 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_286698   java -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 "SKCM-EE-A2MJ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MJ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MJ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000129/*; 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_286698   java -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 "SKCM-EE-A2MK-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MK-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MK-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000130/*; 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_286698   java -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 "SKCM-EE-A2ML-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2ML-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2ML-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000131/*; 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_286698   java -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 "SKCM-EE-A2MM-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MM-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MM-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000132/*; 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_286698   java -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 "SKCM-EE-A2MN-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MN-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MN-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000133/*; 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_286698   java -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 "SKCM-EE-A2MP-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MP-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MP-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000134/*; 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_286698   java -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 "SKCM-EE-A2MQ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MQ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MQ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000135/*; 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_286698   java -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 "SKCM-EE-A2MR-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MR-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MR-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000136/*; 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_286698   java -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 "SKCM-EE-A2MS-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MS-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MS-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000137/*; 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_286698   java -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 "SKCM-EE-A2MT-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MT-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MT-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000138/*; 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_286698   java -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 "SKCM-EE-A2MU-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A2MU-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A2MU-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000139/*; 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_286698   java -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 "SKCM-EE-A3AA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000140/*; 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_286698   java -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 "SKCM-EE-A3AB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000141/*; 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_286698   java -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 "SKCM-EE-A3AC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000142/*; 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_286698   java -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 "SKCM-EE-A3AD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000143/*; 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_286698   java -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 "SKCM-EE-A3AE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000144/*; 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_286698   java -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 "SKCM-EE-A3AF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000145/*; 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_286698   java -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 "SKCM-EE-A3AG-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AG-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AG-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000146/*; 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_286698   java -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 "SKCM-EE-A3AH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3AH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3AH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000147/*; 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_286698   java -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 "SKCM-EE-A3J3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3J3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3J3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000148/*; 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_286698   java -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 "SKCM-EE-A3J4-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3J4-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3J4-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000149/*; 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_286698   java -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 "SKCM-EE-A3J5-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3J5-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3J5-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000150/*; 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_286698   java -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 "SKCM-EE-A3J7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3J7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3J7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000151/*; 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_286698   java -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 "SKCM-EE-A3J8-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3J8-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3J8-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000152/*; 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_286698   java -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 "SKCM-EE-A3JA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000153/*; 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_286698   java -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 "SKCM-EE-A3JB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000154/*; 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_286698   java -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 "SKCM-EE-A3JD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000155/*; 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_286698   java -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 "SKCM-EE-A3JE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000156/*; 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_286698   java -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 "SKCM-EE-A3JH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000157/*; 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_286698   java -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 "SKCM-EE-A3JI-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-EE-A3JI-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EE-A3JI-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000158/*; 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_286698   java -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 "SKCM-ER-A193-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A193-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A193-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000159/*; 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_286698   java -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 "SKCM-ER-A195-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A195-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A195-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000160/*; 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_286698   java -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 "SKCM-ER-A197-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A197-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A197-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000161/*; 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_286698   java -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 "SKCM-ER-A198-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A198-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A198-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000162/*; 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_286698   java -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 "SKCM-ER-A199-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A199-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A199-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000163/*; 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_286698   java -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 "SKCM-ER-A19A-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19A-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19A-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000164/*; 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_286698   java -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 "SKCM-ER-A19B-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19B-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19B-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000165/*; 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_286698   java -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 "SKCM-ER-A19C-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19C-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19C-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000166/*; 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_286698   java -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 "SKCM-ER-A19D-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19D-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19D-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000167/*; 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_286698   java -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 "SKCM-ER-A19E-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19E-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19E-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000168/*; 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_286698   java -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 "SKCM-ER-A19F-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19F-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19F-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000169/*; 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_286698   java -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 "SKCM-ER-A19G-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19G-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19G-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000170/*; 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_286698   java -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 "SKCM-ER-A19H-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19H-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19H-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000171/*; 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_286698   java -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 "SKCM-ER-A19J-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19J-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19J-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000172/*; 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_286698   java -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 "SKCM-ER-A19L-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19L-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19L-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000173/*; 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_286698   java -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 "SKCM-ER-A19N-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19N-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19N-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000174/*; 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_286698   java -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 "SKCM-ER-A19O-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19O-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19O-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000175/*; 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_286698   java -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 "SKCM-ER-A19P-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19P-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19P-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000176/*; 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_286698   java -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 "SKCM-ER-A19Q-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19Q-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19Q-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000177/*; 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_286698   java -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 "SKCM-ER-A19S-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19S-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19S-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000178/*; 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_286698   java -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 "SKCM-ER-A19T-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A19T-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A19T-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000179/*; 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_286698   java -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 "SKCM-ER-A1A1-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A1A1-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A1A1-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000180/*; 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_286698   java -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 "SKCM-ER-A2NC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2NC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2NC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000181/*; 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_286698   java -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 "SKCM-ER-A2ND-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2ND-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2ND-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000182/*; 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_286698   java -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 "SKCM-ER-A2NE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2NE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2NE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000183/*; 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_286698   java -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 "SKCM-ER-A2NF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2NF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2NF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000184/*; 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_286698   java -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 "SKCM-ER-A2NG-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2NG-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2NG-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000185/*; 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_286698   java -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 "SKCM-ER-A2NH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A2NH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A2NH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000186/*; 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_286698   java -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 "SKCM-ER-A3ES-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A3ES-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A3ES-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000187/*; 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_286698   java -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 "SKCM-ER-A3ET-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A3ET-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A3ET-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000188/*; 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_286698   java -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 "SKCM-ER-A3EV-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-ER-A3EV-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-ER-A3EV-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000189/*; 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_286698   java -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 "SKCM-FS-A1YW-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1YW-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1YW-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000190/*; 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_286698   java -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 "SKCM-FS-A1YX-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1YX-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1YX-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000191/*; 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_286698   java -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 "SKCM-FS-A1YY-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1YY-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1YY-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000192/*; 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_286698   java -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 "SKCM-FS-A1Z0-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1Z0-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1Z0-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000193/*; 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_286698   java -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 "SKCM-FS-A1Z3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1Z3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1Z3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000194/*; 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_286698   java -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 "SKCM-FS-A1Z4-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1Z4-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1Z4-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000195/*; 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_286698   java -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 "SKCM-FS-A1Z7-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1Z7-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1Z7-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000196/*; 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_286698   java -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 "SKCM-FS-A1ZA-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZA-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZA-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000197/*; 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_286698   java -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 "SKCM-FS-A1ZB-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZB-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZB-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000198/*; 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_286698   java -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 "SKCM-FS-A1ZC-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZC-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZC-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000199/*; 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_286698   java -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 "SKCM-FS-A1ZD-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZD-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZD-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000200/*; 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_286698   java -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 "SKCM-FS-A1ZE-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZE-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZE-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000201/*; 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_286698   java -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 "SKCM-FS-A1ZF-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZF-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZF-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000202/*; 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_286698   java -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 "SKCM-FS-A1ZG-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZG-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZG-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000203/*; 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_286698   java -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 "SKCM-FS-A1ZH-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZH-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZH-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000204/*; 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_286698   java -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 "SKCM-FS-A1ZJ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZJ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZJ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000205/*; 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_286698   java -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 "SKCM-FS-A1ZK-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZK-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZK-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000206/*; 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_286698   java -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 "SKCM-FS-A1ZM-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZM-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZM-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000207/*; 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_286698   java -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 "SKCM-FS-A1ZP-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZP-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZP-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000208/*; 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_286698   java -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 "SKCM-FS-A1ZQ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZQ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZQ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000209/*; 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_286698   java -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 "SKCM-FS-A1ZR-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZR-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZR-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000210/*; 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_286698   java -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 "SKCM-FS-A1ZS-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZS-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZS-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000211/*; 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_286698   java -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 "SKCM-FS-A1ZT-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZT-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZT-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000212/*; 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_286698   java -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 "SKCM-FS-A1ZU-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZU-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZU-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000213/*; 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_286698   java -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 "SKCM-FS-A1ZW-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZW-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZW-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000214/*; 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_286698   java -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 "SKCM-FS-A1ZY-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZY-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZY-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000215/*; 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_286698   java -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 "SKCM-FS-A1ZZ-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FS-A1ZZ-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FS-A1ZZ-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000216/*; 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_286698   java -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 "SKCM-FW-A3I3-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-FW-A3I3-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-FW-A3I3-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000217/*; 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_286698   java -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 "SKCM-GN-A261-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A261-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A261-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000218/*; 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_286698   java -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 "SKCM-GN-A262-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A262-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A262-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000219/*; 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_286698   java -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 "SKCM-GN-A264-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A264-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A264-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000220/*; 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_286698   java -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 "SKCM-GN-A265-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A265-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A265-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000221/*; 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_286698   java -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 "SKCM-GN-A266-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A266-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A266-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000222/*; 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_286698   java -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 "SKCM-GN-A267-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A267-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A267-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000223/*; 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_286698   java -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 "SKCM-GN-A268-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A268-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A268-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000224/*; 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_286698   java -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 "SKCM-GN-A26A-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A26A-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A26A-06.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286698/iteration1/scatter.0000000225/*; 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_286698   java -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 "SKCM-GN-A26D-TM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "SKCM-GN-A26D-TM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/skcm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-GN-A26D-06.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 19:38:04 2013 in 2.44113778273 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_286698) -J gather_286698 -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/" "SKCM-TM" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/SKCM-TM/2284096/0.MutSigPreprocess.Finished/SKCM-TM.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/SKCM-TM/2284096/0.MutSigPreprocess.Finished/SKCM-TM.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_286698) -J iteration_286698 -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 286698 --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
