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fh_MutSigPreprocess
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/
-i
COAD
-b
hg18
-t
/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
-c
/xchip/cga1/lawrence/db/context65
-bd
/xchip/cga1/annotation/db/ucsc/hg18
-cat
4
-maf1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/maf1.input.tsv
-maf3
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/maf3.input.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/wig1.input.tsv
-wig3
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/wig3.input.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: 'hg18'
                              build_dir: '/xchip/cga1/annotation/db/ucsc/hg18'
             keep_barebones_fields_only: 0
    consolidate_adjacent_muts_threshold: 1
             remove_noncoding_mutations: 1
                    enforce_target_list: 0
                            target_list: [1x64 char]
                     mutation_blacklist: []
                     mutation_whitelist: []

Loading MAFs for Broad
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3807-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3808-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-A6-3810-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3530-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3664-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3666-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3667-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3672-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3673-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3678-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3679-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3680-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3681-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3684-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3685-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3688-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3692-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3693-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3695-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3696-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3710-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3715-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3811-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3812-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3814-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3818-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3819-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3821-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3831-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3833-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3837-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3842-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3844-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3845-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3846-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3848-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3850-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3851-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3852-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3854-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3855-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3856-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3858-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3860-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3864-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3866-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3867-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3869-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3870-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3872-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3875-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3877-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3930-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3939-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3941-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3947-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3949-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3952-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3955-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3956-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3966-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3971-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3972-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3973-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3975-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3976-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3977-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3979-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3980-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3982-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3984-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3986-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3989-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-3994-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A004-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A00N-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A00O-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A010-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A017-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01D-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01I-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01K-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01P-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01R-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01S-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01T-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01V-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01X-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A01Z-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A022-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A024-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A029-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02F-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02H-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02J-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02O-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02W-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A02Y-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A03F-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AA-A03J-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AY-4070-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_COAD.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-AY-4071-01.maf.txt
Loading MAFs for Baylor
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2670-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2672-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2674-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2676-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2677-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2678-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-A6-2683-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3514-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3516-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3517-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3518-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3519-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3520-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3521-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3522-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3524-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3525-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3526-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3527-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3529-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3531-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3532-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3534-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3538-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3542-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3543-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3544-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3548-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3549-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3552-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3553-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3554-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3555-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3556-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3558-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3560-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3561-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-3562-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00A-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00D-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00E-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00F-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00J-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00K-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00L-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00Q-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00R-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00U-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00W-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A00Z-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01F-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01G-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/coad/tracerel__solid_dna__bcm_edu__Level_2__Mutation_Calling__maf/bcm.edu_COAD.SOLiD_DNA.Level_2.1.3.0/TCGA-AA-A01Q-01.maf.txt
Concatenating structs...

                         AAChange: [155]
                         BAM_file: [155]
                     COSMIC_Codon: [155]
                      COSMIC_Gene: [155]
                           Center: [155]
                      ChromChange: [155]
                       Chromosome: [155]
                      Drug_Target: [155]
                     End_position: [155]
                   Entrez_Gene_Id: [155]
                             Exon: [155]
                      Hugo_Symbol: [155]
           Match_Norm_Seq_Allele1: [155]
           Match_Norm_Seq_Allele2: [155]
    Match_Norm_Validation_Allele1: [155]
    Match_Norm_Validation_Allele2: [155]
      Matched_Norm_Sample_Barcode: [155]
                  Mutation_Status: [155]
                       NCBI_Build: [155]
                 Reference_Allele: [155]
                            Score: [155]
                  Sequence_Source: [155]
                        Sequencer: [155]
                 Sequencing_Phase: [155]
                   Start_position: [155]
                           Strand: [155]
                     TranscriptID: [155]
             Tumor_Sample_Barcode: [155]
                Tumor_Seq_Allele1: [155]
                Tumor_Seq_Allele2: [155]
         Tumor_Validation_Allele1: [155]
         Tumor_Validation_Allele2: [155]
                Validation_Method: [155]
                Validation_Status: [155]
           Variant_Classification: [155]
                     Variant_Type: [155]
              Verification_Status: [155]
                          dataset: [155]
                         dbSNP_RS: [155]
                 dbSNP_Val_Status: [155]
                          patient: [155]
                        ----TOTAL: [6355]
Calling preprocess_mutations...
Validation_Status:

      Unknown: [17990]
        Valid: [43458]
     Wildtype: [1112]
    ----TOTAL: [62560]
Removing the following invalidated mutations.
     Wildtype: [1112]
    ----TOTAL: [1112]
Removing the following non-coding mutations (based on "type" field):
        3'UTR: [50]
      5'Flank: [15]
        5'UTR: [24]
          IGR: [80]
       Intron: [759]
          RNA: [48]
    ----TOTAL: [976]
Not enforcing any target list.
Collapsing adjacent mutations:
convert_chr: assuming human for chrX/chrY

       2 SNPs/Indels to one SNP: [1]
    2 redundant SNPs to one SNP: [1]
                      ----TOTAL: [2]

Genes affected:
         TEP1: [1]
        TRIM6: [1]
    ----TOTAL: [2]

Patients affected:
    COAD-AA-3555-TP: [1]
    COAD-AA-A00J-TP: [1]
          ----TOTAL: [2]
convert_chr: assuming human for chrX/chrY
Collapsed 60472 muts to 60470 muts
Getting context: 16% 33% 49% 66% 82% 99% 

Done.
Saved COAD.mutation_preprocessing_report.txt
  [save_struct] 54/62 55/62 56/62 57/62 58/62 59/62 60/62 61/62 62/62  [collapse] [write]
Saved COAD.maf
Total of 155 patients had both MAF and WIG data.
Saved COAD.patients.txt
Saved COAD.coverage.prepare.txt
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/
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/214479
mFile: fh_MutSigPreprocess
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/fh_MutSigPreprocess /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/ -i COAD -b hg18 -t /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt -c /xchip/cga1/lawrence/db/context65 -bd /xchip/cga1/annotation/db/ucsc/hg18 -cat 4 -maf1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/maf1.input.tsv -maf3 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/maf3.input.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/wig1.input.tsv -wig3 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/wig3.input.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
