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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
LUSC
-b
hg19
-t
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
-c
/xchip/cga1/annotation/db/tracks/hg19/c65e
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-cat
4
-maf1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/maf1.input.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/wig1.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: 'hg19'
                              build_dir: '/xchip/cga1/annotation/db/ucsc/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/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3406-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3407-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3408-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3409-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3410-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3411-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3412-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3414-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3415-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3416-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3417-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3419-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3421-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4083-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4086-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4721-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-5592-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-5595-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1070-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1071-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1076-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1077-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1078-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1081-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5782-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5784-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5786-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5787-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-0944-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1002-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1011-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1012-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1016-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4591-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4593-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4595-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4599-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4601-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4604-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4607-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4613-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5471-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5472-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5473-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5474-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5477-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5478-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5480-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5482-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5485-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5489-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5491-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5492-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4532-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4533-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4538-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4547-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4566-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4582-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4583-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4586-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-6737-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2596-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2600-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2608-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5231-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5232-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5234-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5236-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5239-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5240-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5241-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5927-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5928-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5929-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-3783-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-3789-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4133-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4135-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4141-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-5819-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5016-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5019-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5021-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5022-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5024-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5027-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5028-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5029-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5030-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5031-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5035-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5036-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5037-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5039-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-2578-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-3394-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-3920-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-5668-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6143-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6647-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6770-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6771-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3765-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3766-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3767-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3768-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3769-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-6025-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-6026-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4079-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4080-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4081-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-1622-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-5897-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-5898-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-6545-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-6546-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2698-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2707-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2708-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2709-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2710-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2711-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2712-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2713-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2715-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2719-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2720-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2721-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2722-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2723-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2724-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2725-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2726-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-5128-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-5131-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-6202-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2727-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2734-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2742-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2744-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2754-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2755-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2756-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2757-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2758-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2759-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2763-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2765-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2766-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2767-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2768-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2770-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2771-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2773-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2777-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2778-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2780-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2781-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2782-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2783-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2785-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2786-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2787-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2788-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2789-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2791-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2792-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2793-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2794-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2795-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2800-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-70-6722-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-70-6723-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6175-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6560-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6561-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [178]
                                BAM_file: [178]
      CCLE_ONCOMAP_overlapping_mutations: [178]
    CCLE_ONCOMAP_total_mutations_in_gene: [178]
                       CGC_Mutation_Type: [178]
                      CGC_Other_Diseases: [178]
               CGC_Translocation_Partner: [178]
                CGC_Tumor_Types_Germline: [178]
                 CGC_Tumor_Types_Somatic: [178]
                     COSMIC_fusion_genes: [178]
            COSMIC_overlapping_mutations: [178]
            COSMIC_tissue_types_affected: [178]
        COSMIC_total_alterations_in_gene: [178]
                                  Center: [178]
                              Chromosome: [178]
                            Codon_Change: [178]
                     DNARepairGenes_Role: [178]
                             Description: [178]
                                DrugBank: [178]
                            End_position: [178]
                          Entrez_Gene_Id: [178]
        FamilialCancerDatabase_Syndromes: [178]
                   GO_Biological_Process: [178]
                   GO_Cellular_Component: [178]
                   GO_Molecular_Function: [178]
                           Genome_Change: [178]
                             Hugo_Symbol: [178]
                MUTSIG_Published_Results: [178]
                  Match_Norm_Seq_Allele1: [178]
                  Match_Norm_Seq_Allele2: [178]
           Match_Norm_Validation_Allele1: [178]
           Match_Norm_Validation_Allele2: [178]
             Matched_Norm_Sample_Barcode: [178]
                         Mutation_Status: [178]
                              NCBI_Build: [178]
                             OREGANNO_ID: [178]
                         OREGANNO_Values: [178]
                       Other_Transcripts: [178]
                          Protein_Change: [178]
                        Reference_Allele: [178]
                          Refseq_mRNA_Id: [178]
                          Refseq_prot_Id: [178]
                                   Score: [178]
                         Sequence_Source: [178]
                               Sequencer: [178]
                        Sequencing_Phase: [178]
                          Start_position: [178]
                                  Strand: [178]
                        SwissProt_acc_Id: [178]
                      SwissProt_entry_Id: [178]
           TCGAscape_Amplification_Peaks: [178]
                TCGAscape_Deletion_Peaks: [178]
                         Transcript_Exon: [178]
                     Transcript_Position: [178]
                       Transcript_Strand: [178]
                    Tumor_Sample_Barcode: [178]
                       Tumor_Seq_Allele1: [178]
                       Tumor_Seq_Allele2: [178]
                Tumor_Validation_Allele1: [178]
                Tumor_Validation_Allele2: [178]
          Tumorscape_Amplification_Peaks: [178]
               Tumorscape_Deletion_Peaks: [178]
                           UniProt_AApos: [178]
               UniProt_Experimental_Info: [178]
              UniProt_Natural_Variations: [178]
                          UniProt_Region: [178]
                            UniProt_Site: [178]
                       Validation_Method: [178]
                       Validation_Status: [178]
                  Variant_Classification: [178]
                            Variant_Type: [178]
                     Verification_Status: [178]
                             cDNA_Change: [178]
                                 dataset: [178]
                                dbSNP_RS: [178]
                        dbSNP_Val_Status: [178]
                                  filter: [178]
                              gc_content: [178]
                                 patient: [178]
                             ref_context: [178]
                             t_alt_count: [178]
                             t_ref_count: [178]
                   validation_alt_allele: [178]
                       validation_method: [178]
                       validation_status: [178]
                 validation_tumor_sample: [178]
                               ----TOTAL: [15308]
Calling preprocess_mutations...
WARNING: unknown chromosome(s):
    'M'

Validation_Status:

             : [112274]
    ----TOTAL: [112274]
Omitting the following 5 mutations on nonstandard chromosomes:

            M: [5]
    ----TOTAL: [5]
Removing the following non-coding mutations (based on "type" field):
        3'UTR: [1053]
      5'Flank: [1289]
        5'UTR: [492]
          IGR: [18302]
       Intron: [26704]
          RNA: [665]
    ----TOTAL: [48505]
Not enforcing any target list.
Collapsing adjacent mutations:
convert_chr: assuming human for chrX/chrY

    2 SNPs to one Complex_substitution (guessing "Missense"): [16]
                     2 SNPs to one DNP (guessing "Missense"): [848]
                                                   ----TOTAL: [864]

Genes affected:
        ABCA1: [1]
       ABCA10: [1]
        ABCA2: [1]
        ABCA4: [1]
        ABCA9: [1]
       ABCB10: [1]
       ABCC12: [1]
        ABCC8: [1]
        ABCF2: [1]
         ABI1: [1]
         ACP1: [1]
         ACRC: [1]
       ACSM2A: [1]
        ACTA1: [1]
        ACTN4: [1]
       ADAM18: [1]
       ADAM19: [1]
     ADAMTS12: [1]
     ADAMTS17: [1]
      ADAMTS2: [1]
     ADAMTS20: [1]
      ADAMTS9: [1]
     ADAMTSL3: [1]
        ADCY2: [1]
        ADPRH: [1]
       ADRA1A: [1]
         AFF4: [1]
        AGAP3: [1]
       AHNAK2: [1]
       AKAP11: [1]
       AKAP12: [1]
       AKAP13: [1]
        AKAP3: [1]
      ALDH4A1: [1]
      ALDH8A1: [1]
        ALMS1: [1]
        ALPK1: [1]
         ALPL: [1]
      AMAC1L2: [1]
       AMDHD2: [1]
      ANGPTL1: [1]
         ANK2: [1]
         ANK3: [1]
       ANKFN1: [1]
      ANKRD12: [1]
      ANKRD24: [1]
      ANKRD26: [1]
       ANKS1A: [1]
         ANO2: [1]
        ANXA5: [1]
        AP3B1: [1]
        APEX2: [1]
         APOF: [1]
        AQPEP: [1]
      ARFGEF2: [1]
      ARHGDIB: [1]
       ARID1A: [1]
       ARID4B: [1]
      ARL6IP1: [1]
       ARMC10: [1]
         ASB9: [1]
        ASXL1: [1]
         ATN1: [1]
       ATP10A: [1]
       ATP10D: [1]
       ATP11C: [1]
       ATP2B3: [1]
        ATP4A: [1]
     ATP6V0A2: [1]
      ATP6V1A: [1]
       ATPBD4: [1]
          ATR: [1]
        BANK1: [1]
         BAT4: [1]
        BAZ1A: [1]
        BAZ1B: [1]
         BBS9: [1]
       BCL2L1: [1]
       BDKRB2: [1]
        BTBD3: [1]
     C10orf68: [1]
     C10orf88: [1]
     C12orf43: [1]
      C15orf2: [1]
     C19orf47: [1]
     C19orf51: [1]
     C1orf173: [1]
     C20orf20: [1]
     C20orf26: [1]
      C3orf17: [1]
      C3orf20: [1]
        C5AR1: [1]
           C6: [1]
      C6orf58: [1]
          C8A: [1]
      CACNA1I: [1]
       CALCRL: [1]
       CAMTA1: [1]
        CAPN3: [1]
        CAPSL: [1]
       CARD11: [1]
         CASK: [1]
         CASR: [1]
      CCDC105: [1]
      CCDC108: [1]
      CCDC155: [1]
       CCDC57: [1]
       CCDC67: [1]
       CCDC70: [1]
        CCNB3: [1]
        CCRL1: [1]
         CD19: [1]
         CD1A: [1]
       CD40LG: [1]
     CDC42EP4: [1]
        CDCA2: [1]
        CDCP2: [1]
        CDH19: [1]
         CDH9: [1]
        CDKL5: [1]
        CEBPZ: [1]
        CECR1: [1]
        CECR2: [1]
       CEP152: [1]
         CHD8: [1]
         CHGB: [1]
         CILP: [1]
       CLASP2: [1]
        CLCA4: [1]
       CLEC4M: [1]
       CLPTM1: [1]
        CMYA5: [1]
        CNTN3: [1]
         COG4: [1]
      COL19A1: [1]
      COL20A1: [1]
      COL22A1: [1]
       COL4A1: [1]
       COL4A2: [1]
       COL4A5: [1]
       COL4A6: [1]
       COL6A2: [1]
       COL6A6: [1]
       COL7A1: [1]
         COMP: [1]
         CPB2: [1]
         CPS1: [1]
          CR2: [1]
        CRLS1: [1]
        CRYGA: [1]
        CSMD2: [1]
      CSRP2BP: [1]
         CST1: [1]
       CTAGE1: [1]
       CTNNA3: [1]
       CTNNB1: [1]
         CUBN: [1]
        CUZD1: [1]
      CYP2C19: [1]
       CYP4F8: [1]
       CYP7A1: [1]
     DCAF12L1: [1]
     DCAF12L2: [1]
        DCST2: [1]
          DDC: [1]
        DEAF1: [1]
      DEFB118: [1]
         DGKK: [1]
        DHX16: [1]
        DIDO1: [1]
         DLC1: [1]
         DLG2: [1]
       DLGAP1: [1]
         DLK1: [1]
          DMD: [1]
         DMWD: [1]
        DMXL2: [1]
       DNAH11: [1]
        DNAH7: [1]
     DNASE1L1: [1]
       DOCK10: [1]
        DPP10: [1]
         DPP4: [1]
      DPY19L2: [1]
         DPYD: [1]
        DSCAM: [1]
         DSEL: [1]
         DSG4: [1]
         DTX2: [1]
       DUSP10: [1]
         DUXA: [1]
      DYNC2H1: [1]
     DYNC2LI1: [1]
        EFNB1: [1]
        EGLN3: [1]
         EGR2: [1]
       ELAVL2: [1]
        ELTD1: [1]
       ENTPD3: [1]
       ENTPD6: [1]
         ERC1: [1]
         ETV1: [1]
         EXO1: [1]
         EXOG: [1]
        F13A1: [1]
         F13B: [1]
      FAM101B: [1]
      FAM135B: [1]
      FAM153B: [1]
      FAM198B: [1]
      FAM48B1: [1]
       FAM71B: [1]
        FANCG: [1]
         FAT3: [1]
       FBXO43: [1]
        FBXW8: [1]
       FCER1A: [1]
       FCGR2C: [1]
         FGD5: [1]
         FIGN: [1]
         FLNA: [1]
         FMN1: [1]
        FRMD1: [1]
          FRY: [1]
        FSTL1: [1]
         FTCD: [1]
         FTMT: [1]
        FUBP1: [1]
          FYN: [1]
       GABRA2: [1]
        GADL1: [1]
      GALNT10: [1]
      GALNT13: [1]
        GAP43: [1]
       GAS2L2: [1]
        GATA6: [1]
        GCNT2: [1]
        GDF10: [1]
         GDF6: [1]
         GET4: [1]
         GFAP: [1]
        GFPT2: [1]
          GIF: [1]
        GIPC2: [1]
         GJC1: [1]
         GLI2: [1]
       GLT1D1: [1]
       GOLGB1: [1]
       GPR112: [1]
       GPR158: [1]
       GPR174: [1]
       GPR176: [1]
       GPR183: [1]
        GPR77: [1]
        GPR82: [1]
      GRAMD1A: [1]
      GRAMD1C: [1]
        GREM1: [1]
        GRID1: [1]
        GRID2: [1]
        GRIK2: [1]
       GRIN2B: [1]
         GRM3: [1]
         GRM5: [1]
     GTF2IRD1: [1]
      GUCY1A2: [1]
         HBE1: [1]
         HCN1: [1]
          HDC: [1]
     HEATR7B2: [1]
         HELQ: [1]
        HHLA2: [1]
        HIF3A: [1]
     HIST1H1C: [1]
       HIVEP1: [1]
      HLA-DMA: [1]
        HMCN1: [1]
      HNRNPH3: [1]
         HOPX: [1]
        HOXA1: [1]
       HOXC10: [1]
       HOXC12: [1]
          HRG: [1]
       HSD3B1: [1]
        HTR3B: [1]
         HTR7: [1]
          HTT: [1]
        HYDIN: [1]
         IBTK: [1]
          ILK: [1]
         IMP4: [1]
       IMPACT: [1]
         INSR: [1]
        IPO13: [1]
         IRS1: [1]
        ISCA1: [1]
        ISLR2: [1]
        ITGA9: [1]
        ITGAL: [1]
        ITGB8: [1]
        ITPR3: [1]
         JAK3: [1]
       JMJD1C: [1]
         JPH3: [1]
       KCNA10: [1]
        KCND2: [1]
        KCNH4: [1]
        KCNH6: [1]
       KCNK13: [1]
        KCNK3: [1]
        KCNN2: [1]
        KCNQ4: [1]
        KDM4B: [1]
        KDM5B: [1]
     KIAA0100: [1]
     KIAA0947: [1]
     KIAA1210: [1]
     KIAA1274: [1]
     KIAA1462: [1]
     KIAA1586: [1]
     KIAA1841: [1]
     KIAA2022: [1]
       KIF13B: [1]
        KIF19: [1]
        KIF1C: [1]
         KIF7: [1]
      KIRREL2: [1]
        KLHL1: [1]
        KRT77: [1]
        KRT83: [1]
    KRTAP19-5: [1]
     KRTAP5-1: [1]
      L3MBTL4: [1]
        LAMA1: [1]
        LAMA4: [1]
        LAMB4: [1]
        LDOC1: [1]
          LHB: [1]
       LILRB5: [1]
        LRIT3: [1]
        LRRC2: [1]
       LRRC30: [1]
       LRRC55: [1]
       LRRC66: [1]
       LRRIQ3: [1]
        LYZL2: [1]
        LZTR1: [1]
        LZTS1: [1]
       MAD1L1: [1]
         MADD: [1]
       MAGEA6: [1]
       MAGEE2: [1]
       MAP2K3: [1]
        MAPK8: [1]
     MAPK8IP3: [1]
     MAPKAPK2: [1]
      MAPKBP1: [1]
        MAST4: [1]
        MATN2: [1]
        MCCC1: [1]
       MCM3AP: [1]
        MED12: [1]
        MED17: [1]
        MEGF9: [1]
        MEPCE: [1]
        MFAP4: [1]
        MFSD8: [1]
       MGAT4C: [1]
        MGAT5: [1]
       MICAL3: [1]
        MKRN2: [1]
         MLL3: [1]
         MLNR: [1]
          MME: [1]
         MOGS: [1]
        MORC1: [1]
        MOV10: [1]
         MPP4: [1]
       MS4A14: [1]
         MT1H: [1]
         MTOR: [1]
          MTR: [1]
        MUC17: [1]
        MUC5B: [1]
         MUC6: [1]
         MYH1: [1]
        MYH15: [1]
         MYH3: [1]
         MYH6: [1]
        MYLK2: [1]
        MYO10: [1]
       MYO18B: [1]
         MYOF: [1]
        N4BP2: [1]
        NAT8B: [1]
         NBEA: [1]
       NBPF14: [1]
        NCAM2: [1]
         NCAN: [1]
       NCAPH2: [1]
      NCKAP1L: [1]
      NCKAP5L: [1]
        NCOA6: [1]
        NCOR1: [1]
        NFASC: [1]
       NFATC1: [1]
      NGFRAP1: [1]
          NHS: [1]
       NLRP13: [1]
       NLRP14: [1]
        NLRP7: [1]
        NLRP9: [1]
        NLRX1: [1]
       NMNAT2: [1]
         NOD2: [1]
         NOL4: [1]
        NOMO2: [1]
       NOTCH1: [1]
        NRSN1: [1]
        NSUN3: [1]
          NTM: [1]
        NTSR2: [1]
      NUP210L: [1]
        OBSL1: [1]
         ODZ1: [1]
       OR10C1: [1]
       OR10R2: [1]
       OR10Z1: [1]
       OR11L1: [1]
        OR1L4: [1]
        OR1S1: [1]
        OR2L8: [1]
        OR2T4: [1]
        OR2T6: [1]
        OR2W5: [1]
       OR4A15: [1]
       OR4A16: [1]
        OR4M1: [1]
        OR4N2: [1]
        OR4Q3: [1]
       OR51B2: [1]
       OR51Q1: [1]
       OR52E2: [1]
       OR52J3: [1]
       OR56A1: [1]
       OR5AC2: [1]
       OR5AU1: [1]
        OR5H1: [1]
        OR5K3: [1]
        OR5L1: [1]
        OR5M3: [1]
        OR5T1: [1]
        OR6M1: [1]
        OR6T1: [1]
        OR7D4: [1]
        OR8J1: [1]
        OTOP2: [1]
        P2RY4: [1]
         P4HB: [1]
       PABPC3: [1]
       PAPPA2: [1]
         PAX7: [1]
       PCDH15: [1]
        PCDH8: [1]
      PCDHB16: [1]
      PCDHGA6: [1]
         PCLO: [1]
       PCNXL2: [1]
        PCSK6: [1]
         PDCL: [1]
        PDCL2: [1]
        PDCL3: [1]
       PDE10A: [1]
        PDE1C: [1]
        PDE3A: [1]
      PDE4DIP: [1]
        PDE6H: [1]
        PDIA3: [1]
        PDZD2: [1]
        PEG10: [1]
         PES1: [1]
         PFKM: [1]
        PGAP1: [1]
        PGBD3: [1]
      PGLYRP4: [1]
          PGR: [1]
        PHF19: [1]
         PHYH: [1]
      PIK3C2A: [1]
       PIK3CG: [1]
        PLA1A: [1]
        PLCB1: [1]
        PLCE1: [1]
        PLCG2: [1]
       PLCXD1: [1]
         PLD2: [1]
        PLUNC: [1]
        PLVAP: [1]
       PLXNA3: [1]
       PLXNA4: [1]
         PNOC: [1]
        POLA1: [1]
        POLD3: [1]
         POLQ: [1]
         PON1: [1]
        PPEF1: [1]
       PPFIA3: [1]
     PPP1R16B: [1]
      PPP2R1A: [1]
        PREX2: [1]
      PRKCDBP: [1]
        PRPS1: [1]
        PSMF1: [1]
        PTCD1: [1]
       PTPDC1: [1]
       PTPRN2: [1]
        PTPRO: [1]
        PTPRT: [1]
         PXDN: [1]
        PXMP4: [1]
     RALGAPA2: [1]
      RANBP17: [1]
      RAPGEF2: [1]
     RASGEF1B: [1]
       RASSF8: [1]
        RBBP5: [1]
         RBL2: [1]
         RBMX: [1]
        REEP1: [1]
         RELA: [1]
        REXO4: [1]
         RFX6: [1]
        RGS13: [1]
        RIMS1: [1]
        RNFT1: [1]
        ROBO1: [1]
       ROPN1L: [1]
       RPL10L: [1]
        RPLP0: [1]
      RPS6KA2: [1]
         RPS8: [1]
         RTTN: [1]
         SACS: [1]
        SALL4: [1]
       SAMD11: [1]
       SAMD9L: [1]
       SCAPER: [1]
          SCD: [1]
      SCGB2A2: [1]
        SCML4: [1]
        SCN4A: [1]
        SCYL2: [1]
         SDC1: [1]
       SEL1L2: [1]
       SEMA4C: [1]
       SEPT14: [1]
        SEPT7: [1]
     SERPINB4: [1]
       SFMBT2: [1]
        SGIP1: [1]
        SGOL2: [1]
       SH2D4B: [1]
       SHANK3: [1]
         SHC2: [1]
     SIGLEC10: [1]
     SIGLEC12: [1]
     SLC16A10: [1]
      SLC17A4: [1]
      SLC25A2: [1]
     SLC25A46: [1]
      SLC26A7: [1]
      SLC28A1: [1]
      SLC30A8: [1]
      SLC35A4: [1]
      SLC46A1: [1]
       SLC4A8: [1]
       SLC5A3: [1]
      SLC6A11: [1]
       SLC6A5: [1]
       SLC7A4: [1]
       SLC9A8: [1]
       SLC9A9: [1]
      SLCO1B3: [1]
      SLCO2A1: [1]
        SLIT2: [1]
      SMARCA4: [1]
     SMARCAL1: [1]
         SMC3: [1]
         SMC4: [1]
       SMCHD1: [1]
         SNW1: [1]
       SORCS1: [1]
      SPATA20: [1]
         SPEN: [1]
        SPG11: [1]
         SPIC: [1]
         SPZ1: [1]
         SS18: [1]
        STAT4: [1]
       STK32B: [1]
        SYNE2: [1]
         SYNM: [1]
         SYT4: [1]
            T: [1]
         TAF1: [1]
        TAF1A: [1]
        TAF1L: [1]
        TAOK1: [1]
        TAOK2: [1]
       TBC1D7: [1]
        TBX19: [1]
      TCERG1L: [1]
        TCF15: [1]
        TCF25: [1]
        TCL1B: [1]
        TDRD1: [1]
        TDRD3: [1]
       TECPR2: [1]
        TEKT5: [1]
         TEP1: [1]
        TEX15: [1]
       TFAP2B: [1]
         TFE3: [1]
      TGIF2LX: [1]
       THAP10: [1]
        THAP2: [1]
        THSD4: [1]
         THY1: [1]
         TLE2: [1]
         TLK1: [1]
       TM7SF4: [1]
         TMC5: [1]
      TMEM171: [1]
    TMPRSS11B: [1]
        TMTC3: [1]
        TRAT1: [1]
       TRIM15: [1]
       TRIM29: [1]
       TRIM49: [1]
       TRIP12: [1]
        TRPC5: [1]
        TRPM4: [1]
        TRPS1: [1]
        TRPV6: [1]
        TSHZ3: [1]
       TSPAN3: [1]
        TTC14: [1]
       TTC21A: [1]
          TTR: [1]
        TTYH1: [1]
       TUBA3C: [1]
       TUBAL3: [1]
        TUBB4: [1]
         TUT1: [1]
        TYRO3: [1]
         TYW1: [1]
       UBE2Q1: [1]
         UBR4: [1]
      UGT2B10: [1]
         UGT8: [1]
       UMODL1: [1]
      UNC119B: [1]
        UROC1: [1]
         USE1: [1]
         USF2: [1]
      Unknown: [1]
         VARS: [1]
         VASP: [1]
          VIM: [1]
       VPS13C: [1]
         VPS8: [1]
        WDR17: [1]
         WDR3: [1]
        WDR67: [1]
         WIF1: [1]
         WWC3: [1]
         XCL1: [1]
         XKR7: [1]
         XPO4: [1]
         XPOT: [1]
        YIPF1: [1]
        ZDBF2: [1]
      ZDHHC15: [1]
       ZFC3H1: [1]
      ZFYVE19: [1]
      ZFYVE26: [1]
         ZIC1: [1]
       ZNF184: [1]
       ZNF208: [1]
       ZNF236: [1]
       ZNF257: [1]
       ZNF311: [1]
       ZNF318: [1]
       ZNF37A: [1]
        ZNF41: [1]
       ZNF423: [1]
       ZNF425: [1]
       ZNF461: [1]
       ZNF470: [1]
       ZNF479: [1]
       ZNF500: [1]
       ZNF526: [1]
       ZNF561: [1]
       ZNF567: [1]
       ZNF664: [1]
       ZNF668: [1]
       ZNF707: [1]
       ZNF714: [1]
       ZNF778: [1]
      ZNF804B: [1]
       ZNF808: [1]
        ZNFX1: [1]
        ZPLD1: [1]
      ZSCAN10: [1]
      ZSCAN5A: [1]
      ZSCAN5B: [1]
       ABCA13: [2]
      APBB1IP: [2]
         ASPM: [2]
      C9orf72: [2]
      CCDC158: [2]
         CD82: [2]
        CDH10: [2]
        CDH18: [2]
      CNTNAP2: [2]
      CNTNAP5: [2]
          CRP: [2]
        DMBT1: [2]
       DNAH17: [2]
        DNAH5: [2]
        DNAH8: [2]
       DNAJC1: [2]
      EPB41L3: [2]
        EPHA5: [2]
         ESR1: [2]
         FMN2: [2]
        FRAS1: [2]
           GC: [2]
       GRIN3A: [2]
        HERC2: [2]
        HUWE1: [2]
          KDR: [2]
         LRP2: [2]
       MAN2A2: [2]
         MRC2: [2]
        MUC16: [2]
         MUSK: [2]
        NALCN: [2]
          NEB: [2]
        OR2F2: [2]
        OR2G6: [2]
       OR4C16: [2]
        OR4C6: [2]
        OR4M2: [2]
        OR4S2: [2]
        OR8H2: [2]
        OR9Q2: [2]
       PABPC4: [2]
       PARD3B: [2]
      PCDH11X: [2]
       PCDHA1: [2]
        PKHD1: [2]
     PNLIPRP1: [2]
        PRIM2: [2]
         RYR3: [2]
        SCN1A: [2]
      SEC14L2: [2]
        SPTA1: [2]
        SYNE1: [2]
      TMEM131: [2]
          TTN: [2]
        XIRP2: [2]
        CSMD3: [3]
        LRFN5: [3]
         MYH2: [3]
        REG1B: [3]
         RGS7: [3]
         TP53: [3]
         PEG3: [4]
         RYR2: [4]
        USH2A: [4]
        ZFHX4: [6]
    ----TOTAL: [864]

Patients affected:
    LUSC-18-3408-TP: [1]
    LUSC-21-1081-TP: [1]
    LUSC-22-0944-TP: [1]
    LUSC-22-4593-TP: [1]
    LUSC-22-5485-TP: [1]
    LUSC-33-4582-TP: [1]
    LUSC-34-2608-TP: [1]
    LUSC-34-5239-TP: [1]
    LUSC-37-4141-TP: [1]
    LUSC-39-5022-TP: [1]
    LUSC-39-5024-TP: [1]
    LUSC-39-5029-TP: [1]
    LUSC-39-5030-TP: [1]
    LUSC-43-3394-TP: [1]
    LUSC-43-3920-TP: [1]
    LUSC-46-6026-TP: [1]
    LUSC-60-2711-TP: [1]
    LUSC-60-2715-TP: [1]
    LUSC-66-2727-TP: [1]
    LUSC-66-2765-TP: [1]
    LUSC-66-2777-TP: [1]
    LUSC-66-2781-TP: [1]
    LUSC-66-2786-TP: [1]
    LUSC-66-2792-TP: [1]
    LUSC-66-2795-TP: [1]
    LUSC-18-3415-TP: [2]
    LUSC-22-4604-TP: [2]
    LUSC-22-5478-TP: [2]
    LUSC-22-5489-TP: [2]
    LUSC-34-2596-TP: [2]
    LUSC-34-5234-TP: [2]
    LUSC-34-5929-TP: [2]
    LUSC-46-3767-TP: [2]
    LUSC-56-5898-TP: [2]
    LUSC-63-5128-TP: [2]
    LUSC-63-5131-TP: [2]
    LUSC-66-2759-TP: [2]
    LUSC-66-2768-TP: [2]
    LUSC-66-2780-TP: [2]
    LUSC-66-2791-TP: [2]
    LUSC-85-6560-TP: [2]
    LUSC-18-3406-TP: [3]
    LUSC-18-3421-TP: [3]
    LUSC-21-1071-TP: [3]
    LUSC-21-1077-TP: [3]
    LUSC-21-5787-TP: [3]
    LUSC-22-1002-TP: [3]
    LUSC-22-4601-TP: [3]
    LUSC-22-5471-TP: [3]
    LUSC-22-5477-TP: [3]
    LUSC-22-5480-TP: [3]
    LUSC-33-4586-TP: [3]
    LUSC-37-3783-TP: [3]
    LUSC-37-4135-TP: [3]
    LUSC-39-5019-TP: [3]
    LUSC-39-5035-TP: [3]
    LUSC-39-5036-TP: [3]
    LUSC-46-6025-TP: [3]
    LUSC-51-4079-TP: [3]
    LUSC-60-2707-TP: [3]
    LUSC-60-2710-TP: [3]
    LUSC-60-2719-TP: [3]
    LUSC-66-2754-TP: [3]
    LUSC-66-2757-TP: [3]
    LUSC-66-2766-TP: [3]
    LUSC-66-2770-TP: [3]
    LUSC-66-2771-TP: [3]
    LUSC-66-2787-TP: [3]
    LUSC-66-2788-TP: [3]
    LUSC-66-2800-TP: [3]
    LUSC-18-3410-TP: [4]
    LUSC-18-3411-TP: [4]
    LUSC-18-3419-TP: [4]
    LUSC-18-4086-TP: [4]
    LUSC-18-4721-TP: [4]
    LUSC-22-5472-TP: [4]
    LUSC-22-5491-TP: [4]
    LUSC-34-5232-TP: [4]
    LUSC-34-5927-TP: [4]
    LUSC-39-5021-TP: [4]
    LUSC-39-5031-TP: [4]
    LUSC-43-2578-TP: [4]
    LUSC-46-3765-TP: [4]
    LUSC-51-4081-TP: [4]
    LUSC-60-2725-TP: [4]
    LUSC-66-2744-TP: [4]
    LUSC-66-2758-TP: [4]
    LUSC-66-2793-TP: [4]
    LUSC-70-6722-TP: [4]
    LUSC-85-6561-TP: [4]
    LUSC-18-5592-TP: [5]
    LUSC-21-1076-TP: [5]
    LUSC-22-1012-TP: [5]
    LUSC-22-4591-TP: [5]
    LUSC-22-4613-TP: [5]
    LUSC-22-5482-TP: [5]
    LUSC-33-4538-TP: [5]
    LUSC-34-2600-TP: [5]
    LUSC-34-5236-TP: [5]
    LUSC-39-5027-TP: [5]
    LUSC-39-5039-TP: [5]
    LUSC-43-6647-TP: [5]
    LUSC-56-1622-TP: [5]
    LUSC-60-2709-TP: [5]
    LUSC-60-2713-TP: [5]
    LUSC-60-2723-TP: [5]
    LUSC-60-2724-TP: [5]
    LUSC-66-2742-TP: [5]
    LUSC-66-2763-TP: [5]
    LUSC-66-2773-TP: [5]
    LUSC-18-3414-TP: [6]
    LUSC-21-5786-TP: [6]
    LUSC-22-4599-TP: [6]
    LUSC-22-5492-TP: [6]
    LUSC-33-4583-TP: [6]
    LUSC-34-5928-TP: [6]
    LUSC-39-5016-TP: [6]
    LUSC-43-6770-TP: [6]
    LUSC-46-3768-TP: [6]
    LUSC-51-4080-TP: [6]
    LUSC-66-2755-TP: [6]
    LUSC-18-3417-TP: [7]
    LUSC-21-5782-TP: [7]
    LUSC-22-1016-TP: [7]
    LUSC-33-4533-TP: [7]
    LUSC-33-6737-TP: [7]
    LUSC-34-5231-TP: [7]
    LUSC-34-5240-TP: [7]
    LUSC-43-6143-TP: [7]
    LUSC-43-6771-TP: [7]
    LUSC-60-2720-TP: [7]
    LUSC-60-2722-TP: [7]
    LUSC-60-2726-TP: [7]
    LUSC-66-2734-TP: [7]
    LUSC-66-2756-TP: [7]
    LUSC-66-2789-TP: [7]
    LUSC-18-4083-TP: [8]
    LUSC-21-5784-TP: [8]
    LUSC-22-4595-TP: [8]
    LUSC-22-5473-TP: [8]
    LUSC-56-6546-TP: [8]
    LUSC-66-2785-TP: [8]
    LUSC-56-6545-TP: [9]
    LUSC-63-6202-TP: [9]
    LUSC-18-5595-TP: [10]
    LUSC-21-1070-TP: [11]
    LUSC-43-5668-TP: [11]
    LUSC-60-2698-TP: [12]
    LUSC-37-5819-TP: [13]
    LUSC-33-4532-TP: [14]
    LUSC-46-3769-TP: [15]
    LUSC-66-2782-TP: [15]
    LUSC-33-4566-TP: [20]
    LUSC-18-3409-TP: [182]
          ----TOTAL: [864]
convert_chr: assuming human for chrX/chrY
Collapsed 63764 muts to 62900 muts
Getting context: 15% 31% 47% 63% 79% 95% 

Done.
Saved LUSC.mutation_preprocessing_report.txt
  [save_struct] 79/107 80/107 81/107 82/107 83/107 84/107 85/107 86/107 87/107 88/107 89/107 90/107 91/107 92/107 93/107 94/107 95/107 96/107 97/107 98/107 99/107 100/107 101/107 102/107 103/107 104/107 105/107 106/107 107/107  [collapse] [write]
Saved LUSC.maf
Total of 178 patients had both MAF and WIG data.
Saved LUSC.patients.txt
Saved LUSC.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/215210
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 LUSC -b hg19 -t /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt -c /xchip/cga1/annotation/db/tracks/hg19/c65e -bd /xchip/cga1/annotation/db/ucsc/hg19 -cat 4 -maf1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/maf1.input.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/wig1.input.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
