calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1 -E cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && 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/MutSigRun.170.3957/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200
Started submitting scatter jobs at Wed Oct 24 14:57:51 2012
calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000001/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000001/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 1  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000002/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000002/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 2  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000003/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000003/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 3  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000004/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000004/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 4  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000005/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000005/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 5  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000006/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000006/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 6  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000007/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000007/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 7  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000008/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000008/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 8  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000009/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000009/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 9  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000010/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000010/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 10  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000011/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000011/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 11  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000012/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000012/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 12  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000013/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000013/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 13  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000014/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000014/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 14  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000015/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000015/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 15  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000016/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000016/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 16  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000017/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000017/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 17  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000018/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000018/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 18  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000019/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000019/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 19  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000020/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000020/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 20  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000021/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000021/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 21  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000022/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000022/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 22  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000023/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000023/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 23  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000024/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000024/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 24  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000025/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000025/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 25  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000026/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000026/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 26  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000027/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000027/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 27  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000028/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000028/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 28  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000029/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000029/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 29  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000030/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000030/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 30  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000031/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000031/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 31  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000032/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000032/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 32  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000033/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000033/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 33  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000034/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000034/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 34  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000035/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000035/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 35  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000036/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000036/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 36  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000037/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000037/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 37  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000038/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000038/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 38  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000039/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000039/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 39  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000040/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000040/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 40  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000041/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000041/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 41  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000042/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000042/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 42  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000043/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000043/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 43  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000044/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000044/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 44  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000045/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000045/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 45  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000046/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000046/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 46  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000047/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000047/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 47  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000048/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000048/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 48  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000049/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000049/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 49  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000050/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000050/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 50  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000051/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000051/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 51  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000052/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000052/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 52  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000053/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000053/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 53  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000054/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000054/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 54  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000055/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000055/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 55  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000056/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000056/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 56  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000057/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000057/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 57  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000058/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000058/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 58  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000059/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000059/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 59  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000060/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000060/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 60  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000061/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000061/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 61  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000062/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000062/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 62  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000063/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000063/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 63  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000064/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000064/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 64  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000065/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000065/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 65  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000066/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000066/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 66  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000067/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000067/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 67  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000068/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000068/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 68  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000069/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000069/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 69  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000070/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000070/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 70  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000071/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000071/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 71  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000072/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000072/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 72  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000073/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000073/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 73  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000074/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000074/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 74  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000075/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000075/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 75  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000076/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000076/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 76  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000077/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000077/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 77  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000078/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000078/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 78  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000079/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000079/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 79  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000080/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000080/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 80  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000081/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000081/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 81  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000082/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000082/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 82  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000083/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000083/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 83  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000084/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000084/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 84  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000085/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000085/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 85  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000086/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000086/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 86  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000087/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000087/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 87  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000088/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000088/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 88  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000089/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000089/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 89  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000090/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000090/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 90  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000091/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000091/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 91  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000092/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000092/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 92  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000093/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000093/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 93  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000094/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000094/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 94  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000095/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000095/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 95  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000096/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000096/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 96  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000097/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000097/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 97  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000098/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000098/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 98  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000099/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000099/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 99  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000100/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000100/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 100  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000101/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000101/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 101  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000102/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000102/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 102  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000103/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000103/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 103  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000104/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000104/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 104  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000105/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000105/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 105  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000106/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000106/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 106  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000107/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000107/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 107  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000108/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000108/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 108  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000109/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000109/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 109  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000110/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000110/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 110  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000111/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000111/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 111  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000112/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000112/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 112  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000113/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000113/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 113  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000114/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000114/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 114  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000115/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000115/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 115  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000116/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000116/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 116  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000117/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000117/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 117  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000118/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000118/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 118  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000119/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000119/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 119  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000120/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000120/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 120  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000121/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000121/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 121  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000122/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000122/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 122  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000123/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000123/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 123  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000124/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000124/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 124  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000125/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000125/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 125  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000126/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000126/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 126  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000127/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000127/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 127  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000128/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000128/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 128  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000129/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000129/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 129  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000130/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000130/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 130  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000131/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000131/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 131  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000132/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000132/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 132  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000133/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000133/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 133  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000134/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000134/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 134  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000135/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000135/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 135  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000136/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000136/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 136  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000137/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000137/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 137  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000138/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000138/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 138  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000139/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000139/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 139  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000140/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000140/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 140  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000141/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000141/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 141  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000142/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000142/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 142  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000143/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000143/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 143  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000144/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000144/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 144  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000145/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000145/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 145  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000146/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000146/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 146  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000147/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000147/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 147  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000148/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000148/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 148  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000149/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000149/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 149  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000150/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000150/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 150  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000151/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000151/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 151  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000152/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000152/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 152  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000153/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000153/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 153  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000154/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000154/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 154  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000155/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000155/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 155  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000156/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000156/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 156  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000157/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000157/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 157  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000158/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000158/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 158  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000159/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000159/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 159  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000160/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000160/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 160  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000161/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000161/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 161  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000162/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000162/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 162  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000163/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000163/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 163  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000164/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000164/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 164  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000165/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000165/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 165  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000166/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000166/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 166  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000167/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000167/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 167  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000168/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000168/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 168  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000169/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000169/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 169  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000170/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000170/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 170  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000171/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000171/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 171  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000172/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000172/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 172  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000173/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000173/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 173  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000174/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000174/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 174  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000175/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000175/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 175  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000176/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000176/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 176  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000177/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000177/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 177  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000178/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000178/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 178  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000179/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000179/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 179  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000180/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000180/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 180  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000181/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000181/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 181  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000182/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000182/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 182  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000183/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000183/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 183  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000184/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000184/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 184  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000185/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000185/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 185  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000186/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000186/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 186  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000187/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000187/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 187  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000188/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000188/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 188  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000189/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000189/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 189  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000190/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000190/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 190  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000191/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000191/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 191  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000192/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000192/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 192  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000193/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000193/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 193  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000194/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000194/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 194  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000195/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000195/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 195  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000196/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000196/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 196  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000197/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000197/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 197  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000198/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000198/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 198  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000199/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000199/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 199  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

calling:  bsub -r -R rusage[mem=8] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000200/*; echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/iteration1/scatter.0000000200/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215313   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 200  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

Finished submitting scatter jobs at Wed Oct 24 15:04:04 2012 in 6.2121742487 minutes
calling:  bsub -E echo -Xmx2g > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215313/java.opts; cd "/xchip/cga1/annotation" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e scatter-gather.err.txt -o scatter-gather.out.txt -w ended(scatter_215313) -J gather_215313 -P Firehose -R rusage[mem=12] -sp 65   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun   /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 0  -i COAD -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt -genes /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt -b hg18 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg18/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg18 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

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_215313) -J iteration_215313 -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 215313 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
Path iteration1 exists:  True
