
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GDAC_MutSig_Report.36.3965/Mutsig_Report.R")
> result <- main("-L/xchip/tcga/Tools/Nozzle/v1.current", "-dSKCM-TM", "-b/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.bargraphs.png", "-r/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.mutation_breakdown.txt", "-c/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.mutation_rates.txt", "-o/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.covplot.png", "-s/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.sig_genes.txt", "-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.cosmic_sig_genes.txt", "-t/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.cosmic_sig_genes2.txt", "-i/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.cosmic_mutations.txt", "-u/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.clustered_muts.txt", "-g/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.sig_genesets.txt", "-e/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.sig_genesets_2.txt", "-x/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.patients.counts_and_rates.txt", "-v/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.MutSig_version.txt", "-a/xchip/cga/gdac-prod/tcga-gdac/jobResults/CoMut/SKCM-TM/2339411/0.CoMut.Finished/SKCM-TM_coMut.png", "-f/xchip/cga/gdac-prod/tcga-gdac/jobResults/CoMut/SKCM-TM/2339411/0.CoMut.Finished/SKCM-TM_coMut.pdf", "-h/xchip/cga/gdac-prod/tcga-gdac/jobResults/GenerateStickFigures/SKCM-TM/2339412/0.GenerateStickFigures.Finished/generatedStickFigurePaths.txt", "-j/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.final_analysis_set.maf", "-k/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/SKCM-TM/2335464/0.MutSigPreprocess.Finished/SKCM-TM.mutation_preprocessing_report.txt", "-n/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2337578/0.MutSigRun.Finished/SKCM-TM.mutation_filtering_report.txt")
> q(save="no")
