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fh_MutSigPreprocess
-i
PRAD
-b
hg19
-t
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
-c
/xchip/cga1/annotation/db/tracks/hg19/c65e
-cw
no_longer_needed
-cat
4
-maf1
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis276234062200798647.att_dependentsValues8665707765758208253.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis760244379092734753.att_dependentsValues7659201597281790844.tsv
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt

               perform_mutsig2_analysis: 1
     use_sample_specific_mutation_rates: 1
        analyze_silent_nonsilent_ratios: 1
                 sig_calculation_method: 'projection'
                           print_report: 0
                  clip_tumor_from_names: 1
                                  build: 'hg19'
             keep_barebones_fields_only: 0
    consolidate_adjacent_muts_threshold: 1
             remove_noncoding_mutations: 1
                    enforce_target_list: 0
                            target_list: [1x69 char]
                     mutation_blacklist: []
                     mutation_whitelist: []

Loading MAFs for Broad
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5737-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5738-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5739-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5740-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5741-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5743-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5744-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5745-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5746-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5748-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5750-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5751-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5752-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5753-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5754-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5761-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5762-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5763-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5764-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5765-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5766-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5767-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5768-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5769-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5771-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5772-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5788-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5789-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5790-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5791-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5792-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5794-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5494-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5495-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5496-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5497-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5498-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5499-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5501-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5502-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5503-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5504-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5505-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5506-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5507-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5508-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5509-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5510-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5511-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5512-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5514-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5515-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5516-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5517-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5518-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5519-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5521-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5522-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5524-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5525-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5526-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5527-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5530-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5531-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5532-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5542-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6332-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6336-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6348-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6356-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6362-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6363-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6364-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6365-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6367-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6370-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6371-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6373-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6378-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6384-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6385-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6494-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6496-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [83]
                                BAM_file: [83]
      CCLE_ONCOMAP_overlapping_mutations: [83]
    CCLE_ONCOMAP_total_mutations_in_gene: [83]
                       CGC_Mutation_Type: [83]
                      CGC_Other_Diseases: [83]
               CGC_Translocation_Partner: [83]
                CGC_Tumor_Types_Germline: [83]
                 CGC_Tumor_Types_Somatic: [83]
                     COSMIC_fusion_genes: [83]
            COSMIC_overlapping_mutations: [83]
            COSMIC_tissue_types_affected: [83]
        COSMIC_total_alterations_in_gene: [83]
                                  Center: [83]
                              Chromosome: [83]
                            Codon_Change: [83]
                     DNARepairGenes_Role: [83]
                             Description: [83]
                                DrugBank: [83]
                            End_position: [83]
                          Entrez_Gene_Id: [83]
        FamilialCancerDatabase_Syndromes: [83]
                   GO_Biological_Process: [83]
                   GO_Cellular_Component: [83]
                   GO_Molecular_Function: [83]
                           Genome_Change: [83]
                             Hugo_Symbol: [83]
                MUTSIG_Published_Results: [83]
                  Match_Norm_Seq_Allele1: [83]
                  Match_Norm_Seq_Allele2: [83]
           Match_Norm_Validation_Allele1: [83]
           Match_Norm_Validation_Allele2: [83]
             Matched_Norm_Sample_Barcode: [83]
                         Mutation_Status: [83]
                              NCBI_Build: [83]
                             OREGANNO_ID: [83]
                         OREGANNO_Values: [83]
                       Other_Transcripts: [83]
                          Protein_Change: [83]
                        Reference_Allele: [83]
                          Refseq_mRNA_Id: [83]
                          Refseq_prot_Id: [83]
                                   Score: [83]
                         Sequence_Source: [83]
                               Sequencer: [83]
                        Sequencing_Phase: [83]
                          Start_position: [83]
                                  Strand: [83]
                        SwissProt_acc_Id: [83]
                      SwissProt_entry_Id: [83]
           TCGAscape_Amplification_Peaks: [83]
                TCGAscape_Deletion_Peaks: [83]
                         Transcript_Exon: [83]
                     Transcript_Position: [83]
                       Transcript_Strand: [83]
                    Tumor_Sample_Barcode: [83]
                       Tumor_Seq_Allele1: [83]
                       Tumor_Seq_Allele2: [83]
                Tumor_Validation_Allele1: [83]
                Tumor_Validation_Allele2: [83]
          Tumorscape_Amplification_Peaks: [83]
               Tumorscape_Deletion_Peaks: [83]
                           UniProt_AApos: [83]
               UniProt_Experimental_Info: [83]
              UniProt_Natural_Variations: [83]
                          UniProt_Region: [83]
                            UniProt_Site: [83]
                       Validation_Method: [83]
                       Validation_Status: [83]
                  Variant_Classification: [83]
                            Variant_Type: [83]
                     Verification_Status: [83]
                             cDNA_Change: [83]
                                 dataset: [83]
                                dbSNP_RS: [83]
                        dbSNP_Val_Status: [83]
                                  filter: [83]
                              gc_content: [83]
                                 patient: [83]
                             ref_context: [83]
                             t_alt_count: [83]
                             t_ref_count: [83]
                   validation_alt_allele: [83]
                       validation_method: [83]
                       validation_status: [83]
                 validation_tumor_sample: [83]
                               ----TOTAL: [7138]
Calling preprocess_mutations...
Validation_Status:

             : [12281]
    ----TOTAL: [12281]
Removing the following non-coding mutations (based on "type" field):
        3'UTR: [685]
      5'Flank: [167]
        5'UTR: [240]
          IGR: [974]
       Intron: [4298]
          RNA: [320]
    ----TOTAL: [6684]
Not enforcing any target list.
Collapsing adjacent mutations:

    2 SNPs to one Complex_substitution (guessing "Missense"): [2]
                     2 SNPs to one DNP (guessing "Missense"): [27]
                                                   ----TOTAL: [29]

Genes affected:
          AGK: [1]
     C9orf100: [1]
     CCDC144B: [1]
        CCDC7: [1]
         CRB2: [1]
         CSH2: [1]
        FOXN1: [1]
      GALNTL5: [1]
        HDAC6: [1]
      KHDRBS3: [1]
    KRTAP4-11: [1]
     KRTAP4-7: [1]
        LCE1F: [1]
        MKLN1: [1]
       MRPL50: [1]
        MUC16: [1]
        NCOA4: [1]
       NOTCH2: [1]
       NUSAP1: [1]
        PRSS3: [1]
    RPL23AP32: [1]
       SDHAP2: [1]
        SFRS2: [1]
        ZMYM3: [1]
       ZNF323: [1]
        CHEK2: [2]
      Unknown: [2]
    ----TOTAL: [29]

Patients affected:
    PRAD-CH-5750: [1]
    PRAD-CH-5764: [1]
    PRAD-CH-5765: [1]
    PRAD-CH-5789: [1]
    PRAD-EJ-5494: [1]
    PRAD-EJ-5495: [1]
    PRAD-EJ-5497: [1]
    PRAD-EJ-5499: [1]
    PRAD-EJ-5504: [1]
    PRAD-EJ-5510: [1]
    PRAD-EJ-5512: [1]
    PRAD-EJ-5518: [1]
    PRAD-EJ-5524: [1]
    PRAD-EJ-5525: [1]
    PRAD-G9-6365: [1]
    PRAD-G9-6370: [1]
    PRAD-CH-5754: [2]
    PRAD-G9-6336: [2]
    PRAD-G9-6348: [2]
    PRAD-G9-6362: [2]
    PRAD-G9-6364: [2]
    PRAD-CH-5792: [3]
       ----TOTAL: [29]
Collapsed 5597 muts to 5568 muts
Getting context: 2/5568 values in FWB were undefined (-1): these have been changed to NaN in the returned array.

Done.
Saved PRAD.mutation_preprocessing_report.txt
Saved PRAD.maf
Total of 83 patients had both MAF and WIG data.
Saved PRAD.patients.txt
Saved PRAD.coverage.prepare.txt
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142918
mFile: fh_MutSigPreprocess
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/fh_MutSigPreprocess -i PRAD -b hg19 -t /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt -c /xchip/cga1/annotation/db/tracks/hg19/c65e -cw no_longer_needed -cat 4 -maf1 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis276234062200798647.att_dependentsValues8665707765758208253.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis760244379092734753.att_dependentsValues7659201597281790844.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
