
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_MutSig_Report/broadinstitute.org/cancer.genome.analysis/00412/43/Mutsig_Report.R")
> result <- main("-L/xchip/tcga/Tools/Nozzle/v1.current", "-dLAML-TB", "-b/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.bargraphs.png", "-r/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.mutation_breakdown.txt", "-c/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.mutation_rates.txt", "-o/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.covplot.png", "-s/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.sig_genes.txt", "-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.cosmic_sig_genes.txt", "-t/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.cosmic_sig_genes2.txt", "-i/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.cosmic_mutations.txt", "-u/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.clustered_muts.txt", "-g/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.sig_genesets.txt", "-e/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.sig_genesets_2.txt", "-x/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.patients.counts_and_rates.txt", "-v/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.MutSig_version.txt", "-a/xchip/cga/gdac-prod/tcga-gdac/jobResults/CoMut/LAML-TB/4474553/LAML-TB_coMut.png", "-f/xchip/cga/gdac-prod/tcga-gdac/jobResults/CoMut/LAML-TB/4474553/LAML-TB_coMut.pdf", "-h/xchip/cga/gdac-prod/tcga-gdac/jobResults/GenerateStickFigures/LAML-TB/4474551/generatedStickFigurePaths.txt", "-j/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.final_analysis_set.maf", "-k/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LAML-TB/4469887/LAML-TB.mutation_preprocessing_report.txt", "-n/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LAML-TB/4473913/LAML-TB.mutation_filtering_report.txt", "-p/xchip/cga/gdac-prod/tcga-gdac/jobResults/lego_plotter/LAML-TB/4474550/LAML-TB.final_analysis_set.maf.mutation_profile.png", "-q/xchip/cga/gdac-prod/tcga-gdac/jobResults/lego_plotter/LAML-TB/4474550/LAML-TB.final_analysis_set.maf.mutation_profile_AF.png", "-w/xchip/cga/gdac-prod/tcga-gdac/jobResults/lego_plotter/LAML-TB/4474550/LAML-TB.final_analysis_set.maf.mutation_profile.ai", "-y/xchip/cga/gdac-prod/tcga-gdac/jobResults/lego_plotter/LAML-TB/4474550/LAML-TB.final_analysis_set.maf.mutation_profile_AF.ai")
> q(save="no")
