Warning: No display specified.  You will not be able to display graphics on the screen.
fh_MutSigPreprocess
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/
-i
GBM-TP
-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/GBM-TP/2283735/maf1.input.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM-TP/2283735/wig1.input.tsv
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0_cga.pancan.blacklist.v7.hg19.params.txt

                     mutation_blacklist: [1x73 char]
               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_whitelist: []

Loading MAFs for Broad
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0003-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0033-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0047-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-0055-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2470-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2483-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2485-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-02-2486-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0119-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0122-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0124-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0125-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0126-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0128-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0129-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0130-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0132-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0137-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0139-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0140-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0141-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0142-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0145-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0151-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0152-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0154-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0155-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0157-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0158-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0165-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0166-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0167-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0168-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0169-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0171-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0173-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0174-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0178-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0184-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0185-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0188-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0189-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0190-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0192-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0195-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0209-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0210-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0211-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0213-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0214-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0216-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0219-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0221-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0237-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0238-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0240-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0241-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0644-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0645-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0646-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0648-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0649-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0650-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0686-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0743-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0744-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0745-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0747-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0749-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0750-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0875-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0876-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0877-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0878-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0879-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0881-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0882-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-0939-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-1804-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-1806-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2557-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2558-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2559-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2561-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2562-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2563-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2564-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2565-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2567-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2569-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-2570-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5408-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5410-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5411-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5412-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5413-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5414-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5415-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5417-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5418-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5856-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5858-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-5859-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6388-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6389-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6390-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6391-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6693-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6694-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6695-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6697-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6698-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6699-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6700-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-06-6701-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-08-0386-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0615-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0616-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0618-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0619-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0688-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0692-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-0821-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-1597-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3649-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3650-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3652-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-3653-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5295-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5299-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-12-5301-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0740-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0781-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0786-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0787-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0789-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0790-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0813-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0817-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0862-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-0871-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1034-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1043-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1395-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1450-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1456-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1823-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1825-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-1829-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-2554-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-3476-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-14-4157-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-15-0742-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-15-1444-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-0846-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-0861-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-1045-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-16-1048-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-1390-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-1790-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2619-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2620-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2623-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2624-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2625-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2629-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-2631-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-4068-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5947-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5950-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5951-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5952-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5953-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5954-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5955-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5958-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5959-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-19-5960-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-1439-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-1442-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5132-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5133-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5134-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5135-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5136-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-5139-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-6173-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-26-6174-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1830-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1831-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1832-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1833-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1834-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1835-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1836-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1837-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-1838-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2518-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2519-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2521-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2523-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2524-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2526-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2527-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-27-2528-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-1747-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-1753-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2499-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2501-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2502-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2509-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2510-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2513-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-2514-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5204-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5207-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5208-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5209-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5211-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5213-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5214-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5215-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5216-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5218-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5219-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-5220-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-28-6450-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1970-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1977-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1979-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1980-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1982-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1986-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-1991-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2491-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2494-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2495-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2498-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2615-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2632-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2634-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-2638-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4208-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4209-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4210-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4211-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4213-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-4719-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-32-5222-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2571-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2572-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2573-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-2575-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3392-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3393-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-3915-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-4097-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-5651-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-41-6646-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6573-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6575-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6577-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6578-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-74-6584-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4925-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4926-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4927-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4928-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4929-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4931-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4932-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4934-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-4935-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6191-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6192-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6193-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6280-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6282-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6283-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6285-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6286-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6656-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6657-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6660-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6661-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6662-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6663-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-76-6664-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-81-5910-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-81-5911-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/gbm/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.2.5.0/TCGA-87-5896-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [291]
                                BAM_file: [291]
      CCLE_ONCOMAP_overlapping_mutations: [291]
    CCLE_ONCOMAP_total_mutations_in_gene: [291]
                       CGC_Mutation_Type: [291]
                      CGC_Other_Diseases: [291]
               CGC_Translocation_Partner: [291]
                CGC_Tumor_Types_Germline: [291]
                 CGC_Tumor_Types_Somatic: [291]
                     COSMIC_fusion_genes: [291]
            COSMIC_overlapping_mutations: [291]
            COSMIC_tissue_types_affected: [291]
        COSMIC_total_alterations_in_gene: [291]
                                  Center: [291]
                              Chromosome: [291]
                            Codon_Change: [291]
                     DNARepairGenes_Role: [291]
                             Description: [291]
                                DrugBank: [291]
                            End_position: [291]
                          Entrez_Gene_Id: [291]
        FamilialCancerDatabase_Syndromes: [291]
                   GO_Biological_Process: [291]
                   GO_Cellular_Component: [291]
                   GO_Molecular_Function: [291]
                           Genome_Change: [291]
                             Hugo_Symbol: [291]
                MUTSIG_Published_Results: [291]
                  Match_Norm_Seq_Allele1: [291]
                  Match_Norm_Seq_Allele2: [291]
           Match_Norm_Validation_Allele1: [291]
           Match_Norm_Validation_Allele2: [291]
             Matched_Norm_Sample_Barcode: [291]
                         Mutation_Status: [291]
                              NCBI_Build: [291]
                             OREGANNO_ID: [291]
                         OREGANNO_Values: [291]
                       Other_Transcripts: [291]
                          Protein_Change: [291]
                        Reference_Allele: [291]
                          Refseq_mRNA_Id: [291]
                          Refseq_prot_Id: [291]
                                   Score: [291]
                         Sequence_Source: [291]
                               Sequencer: [291]
                        Sequencing_Phase: [291]
                          Start_position: [291]
                                  Strand: [291]
                        SwissProt_acc_Id: [291]
                      SwissProt_entry_Id: [291]
           TCGAscape_Amplification_Peaks: [291]
                TCGAscape_Deletion_Peaks: [291]
                         Transcript_Exon: [291]
                     Transcript_Position: [291]
                       Transcript_Strand: [291]
                    Tumor_Sample_Barcode: [291]
                       Tumor_Seq_Allele1: [291]
                       Tumor_Seq_Allele2: [291]
                Tumor_Validation_Allele1: [291]
                Tumor_Validation_Allele2: [291]
          Tumorscape_Amplification_Peaks: [291]
               Tumorscape_Deletion_Peaks: [291]
                           UniProt_AApos: [291]
               UniProt_Experimental_Info: [291]
              UniProt_Natural_Variations: [291]
                          UniProt_Region: [291]
                            UniProt_Site: [291]
                       Validation_Method: [291]
                       Validation_Status: [291]
                  Variant_Classification: [291]
                            Variant_Type: [291]
                     Verification_Status: [291]
                             cDNA_Change: [291]
                                   categ: [291]
               categ_ignoring_null_categ: [291]
                                     chr: [291]
                          classification: [291]
                               context65: [291]
                            context_orig: [291]
                                 dataset: [291]
                                dbSNP_RS: [291]
                        dbSNP_Val_Status: [291]
                                     end: [291]
                              gc_content: [291]
                                    gene: [291]
                                gene_idx: [291]
                    i_ACHILLES_Top_Genes: [291]
        i_CCLE_SEQ_overlapping_mutations: [291]
      i_CCLE_SEQ_total_mutations_in_gene: [291]
                            i_init_t_lod: [291]
                             i_judgement: [291]
                            i_t_ALT_F1R2: [291]
                            i_t_ALT_F2R1: [291]
                               i_t_Foxog: [291]
                            i_t_REF_F1R2: [291]
                            i_t_REF_F2R1: [291]
                           i_t_lod_fstar: [291]
                               i_tumor_f: [291]
                               is_coding: [291]
                                  is_del: [291]
                                is_flank: [291]
                                is_indel: [291]
                                  is_ins: [291]
                             is_missense: [291]
                             is_nonsense: [291]
                               is_silent: [291]
                               is_splice: [291]
                                 newbase: [291]
                                 pat_idx: [291]
                                 patient: [291]
                              ref_allele: [291]
                             ref_context: [291]
                                   start: [291]
                             t_alt_count: [291]
                             t_ref_count: [291]
                             tum_allele1: [291]
                             tum_allele2: [291]
                                    type: [291]
                   validation_alt_allele: [291]
                       validation_method: [291]
                       validation_status: [291]
                 validation_tumor_sample: [291]
                               ----TOTAL: [35502]
Calling preprocess_mutations...
Validation_Status:

             : [21540]
    ----TOTAL: [21540]
Applying mutation blacklist:  /xchip/cga1/reference/mutsig_params/pancan_mutation_blacklist.v7.hg19.txt
WARNING: unknown chromosome(s):
    {''}

WARNING: chromosome number(s) out of range for this genome
     0

{Warning: The KEYBOARD function cannot be used in compiled applications.} 
> In keyboard at 4
  In convert_chr at 104
  In add_and_convert_simple_fieldnames at 32
  In preprocess_mutations at 77
  In fh_MutSigPreprocess at 200
Omitting the following 126 blacklisted mutations:
    'GBM-02-0047-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-02-0055-TP'    'ZNF534'       [19]    [ 52942411]    'A' 
    'GBM-02-2485-TP'    'SFRP1'        [ 8]    [ 41166547]    'T' 
    'GBM-02-2485-TP'    'SIGLEC8'      [19]    [ 51961617]    '-' 
    'GBM-06-0124-TP'    'ANKRD36'      [ 2]    [ 97869931]    'T' 
    'GBM-06-0129-TP'    'SIN3A'        [15]    [ 75705213]    'G' 
    'GBM-06-0129-TP'    'PCDHA10'      [ 5]    [140237249]    'C' 
    'GBM-06-0142-TP'    'POTEC'        [18]    [ 14513675]    'C' 
    'GBM-06-0145-TP'    'SEMG1'        [20]    [ 43837278]    'A' 
    'GBM-06-0152-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-06-0157-TP'    'ZNF845'       [19]    [ 53856730]    'A' 
    'GBM-06-0158-TP'    'ZNF814'       [19]    [ 58385762]    'G' 
    'GBM-06-0173-TP'    'UGT1A8'       [ 2]    [234526363]    'G' 
    'GBM-06-0173-TP'    'SRP19'        [ 5]    [112227939]    'C' 
    'GBM-06-0174-TP'    'LRP3'         [19]    [ 33695616]    'C' 
    'GBM-06-0174-TP'    'MACF1'        [ 1]    [ 39799059]    'G' 
    'GBM-06-0184-TP'    'RB1'          [13]    [ 49033839]    'T' 
    'GBM-06-0185-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-06-0190-TP'    'LRP3'         [19]    [ 33695616]    'C' 
    'GBM-06-0213-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-06-0213-TP'    'LRP3'         [19]    [ 33695616]    'C' 
    'GBM-06-0216-TP'    'RERE'         [ 1]    [  8420616]    'G' 
    'GBM-06-0237-TP'    'NBPF1'        [ 1]    [ 16918653]    'T' 
    'GBM-06-0237-TP'    'MAMLD1'       [23]    [149639325]    '-' 
    'GBM-06-0646-TP'    'NBPF10'       [ 1]    [145367739]    'G' 
    'GBM-06-0646-TP'    'CADM1'        [11]    [115080343]    'T' 
    'GBM-06-0646-TP'    'DRD5'         [ 4]    [  9784478]    'A' 
    'GBM-06-0648-TP'    'MUC4'         [ 3]    [195505836]    'C' 
    'GBM-06-0649-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-06-0744-TP'    'ZNF534'       [19]    [ 52942423]    'A' 
    'GBM-06-0750-TP'    'ARHGAP11B'    [15]    [ 30938316]    'A' 
    'GBM-06-2558-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-06-2570-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-06-5414-TP'    'POTEC'        [18]    [ 14513675]    'C' 
    'GBM-06-5418-TP'    'ZNF814'       [19]    [ 58385762]    'G' 
    'GBM-06-6388-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-06-6389-TP'    'KRTAP4-11'    [17]    [ 39274415]    'T' 
    'GBM-06-6693-TP'    'PRAMEF11'     [ 1]    [ 12885289]    'T' 
    'GBM-06-6695-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-06-6697-TP'    'ANKRD36'      [ 2]    [ 97869931]    'T' 
    'GBM-06-6700-TP'    'KRTAP1-1'     [17]    [ 39197393]    'C' 
    'GBM-12-0616-TP'    'USP11'        [23]    [ 47104414]    'C' 
    'GBM-12-0619-TP'    'RB1'          [13]    [ 49033844]    'T' 
    'GBM-12-0619-TP'    'ANKRD36'      [ 2]    [ 97869931]    'T' 
    'GBM-12-0821-TP'    'MYPOP'        [19]    [ 46393971]    'G' 
    'GBM-12-3649-TP'    'NBPF10'       [ 1]    [145367739]    'G' 
    'GBM-12-3649-TP'    'ZNF534'       [19]    [ 52942423]    'A' 
    'GBM-12-5299-TP'    'ARSD'         [23]    [  2836003]    'A' 
    'GBM-14-0781-TP'    'KRTAP4-7'     [17]    [ 39240819]    'G' 
    'GBM-14-0787-TP'    'KRTAP5-4'     [11]    [  1642817]    'G' 
    'GBM-14-0787-TP'    'KRTAP5-4'     [11]    [  1642827]    'C' 
    'GBM-14-0787-TP'    'RGPD3'        [ 2]    [107049631]    'T' 
    'GBM-14-0789-TP'    'LRP3'         [19]    [ 33695616]    'C' 
    'GBM-14-0789-TP'    'ZNF534'       [19]    [ 52942411]    'A' 
    'GBM-14-0871-TP'    'LRP3'         [19]    [ 33695616]    'C' 
    'GBM-14-1043-TP'    'KRTAP4-11'    [17]    [ 39274291]    'C' 
    'GBM-14-1450-TP'    'CHEK2'        [22]    [ 29091840]    'CA'
    'GBM-14-1456-TP'    'KRTAP4-11'    [17]    [ 39274319]    'C' 
    'GBM-14-1823-TP'    'ANKRD36'      [ 2]    [ 97869931]    'T' 
    'GBM-14-1829-TP'    'NAB2'         [12]    [ 57485446]    'C' 
    'GBM-14-3476-TP'    'DRD5'         [ 4]    [  9784478]    'A' 
    'GBM-16-0846-TP'    'USP11'        [23]    [ 47104414]    'C' 
    'GBM-16-1045-TP'    'TPRN'         [ 9]    [140086816]    'T' 
    'GBM-16-1048-TP'    'KRTAP4-7'     [17]    [ 39240819]    'G' 
    'GBM-16-1048-TP'    'KRTAP4-7'     [17]    [ 39240900]    'G' 
    'GBM-19-2619-TP'    'MST1'         [ 3]    [ 49723522]    'A' 
    'GBM-19-2619-TP'    'FLG2'         [ 1]    [152324558]    '-' 
    'GBM-19-2629-TP'    'KRTAP4-8'     [17]    [ 39254054]    'T' 
    'GBM-19-2631-TP'    'ZNF814'       [19]    [ 58385762]    'G' 
    'GBM-19-4068-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-19-5950-TP'    'MUC4'         [ 3]    [195505836]    'C' 
    'GBM-19-5952-TP'    'NBPF10'       [ 1]    [145367739]    'G' 
    'GBM-19-5953-TP'    'ZNF845'       [19]    [ 53856702]    'A' 
    'GBM-19-5955-TP'    'KRTAP4-9'     [17]    [ 39261693]    'T' 
    'GBM-19-5958-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-19-5958-TP'    'PCDHB8'       [ 5]    [140559327]    'T' 
    'GBM-19-5959-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-26-5134-TP'    'IRS2'         [13]    [110434967]    'G' 
    'GBM-26-5136-TP'    'KRTAP4-11'    [17]    [ 39274087]    'C' 
    'GBM-26-6174-TP'    'MUC4'         [ 3]    [195505836]    'C' 
    'GBM-26-6174-TP'    'UGT2B10'      [ 4]    [ 69870669]    'A' 
    'GBM-27-1832-TP'    'POTEC'        [18]    [ 14513675]    'C' 
    'GBM-27-1832-TP'    'POTEC'        [18]    [ 14513764]    'T' 
    'GBM-27-1832-TP'    'ANKRD36'      [ 2]    [ 97869931]    'T' 
    'GBM-27-1835-TP'    'KRTAP4-8'     [17]    [ 39254054]    'T' 
    'GBM-27-2519-TP'    'KRTAP4-8'     [17]    [ 39254021]    'T' 
    'GBM-27-2527-TP'    'MUC4'         [ 3]    [195505813]    'C' 
    'GBM-27-2528-TP'    'KRTAP4-7'     [17]    [ 39240908]    'C' 
    'GBM-28-1753-TP'    'POTEC'        [18]    [ 14513764]    'T' 
    'GBM-28-2501-TP'    'KRTAP4-9'     [17]    [ 39261693]    'T' 
    'GBM-28-2510-TP'    'KRTAP4-5'     [17]    [ 39305619]    'T' 
    'GBM-28-2514-TP'    'CADM1'        [11]    [115080343]    'T' 
    'GBM-28-2514-TP'    'FLG2'         [ 1]    [152324558]    '-' 
    'GBM-28-5208-TP'    'KRTAP5-4'     [11]    [  1642827]    'C' 
    'GBM-28-5211-TP'    'MUC4'         [ 3]    [195505836]    'C' 
    'GBM-28-5214-TP'    'UGT2B10'      [ 4]    [ 69870669]    'A' 
    'GBM-28-6450-TP'    'NBPF10'       [ 1]    [145367739]    'G' 
    'GBM-32-1977-TP'    'KCNB1'        [20]    [ 48098748]    'T' 
    'GBM-32-1986-TP'    'CHEK2'        [22]    [ 29091840]    'CA'
    'GBM-32-1991-TP'    'ALG1L2'       [ 3]    [129811972]    'C' 
    'GBM-32-2491-TP'    'POTEC'        [18]    [ 14513764]    'T' 
    'GBM-32-2495-TP'    'ZNF814'       [19]    [ 58385748]    'A' 
    'GBM-32-2498-TP'    'CHEK2'        [22]    [ 29091840]    'CA'
    'GBM-32-2615-TP'    'KRTAP4-7'     [17]    [ 39240900]    'G' 
    'GBM-32-2615-TP'    'KRTAP4-7'     [17]    [ 39240908]    'C' 
    'GBM-32-2615-TP'    'KRTAP4-9'     [17]    [ 39261693]    'T' 
    'GBM-32-2632-TP'    'POTEC'        [18]    [ 14513764]    'T' 
    'GBM-32-4211-TP'    'KRTAP4-9'     [17]    [ 39261693]    'T' 
    'GBM-32-4211-TP'    'RGPD3'        [ 2]    [107049631]    'T' 
    'GBM-32-5222-TP'    'MUC4'         [ 3]    [195515449]    'T' 
    'GBM-41-2571-TP'    'CHEK2'        [22]    [ 29091840]    'CA'
    'GBM-41-2575-TP'    'UGT2B10'      [ 4]    [ 69870669]    'A' 
    'GBM-41-3392-TP'    'MUC4'         [ 3]    [195505836]    'C' 
    'GBM-41-3915-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-74-6575-TP'    'POTEC'        [18]    [ 14513675]    'C' 
    'GBM-76-4934-TP'    'OR4Q3'        [14]    [ 20215929]    'AG'
    'GBM-76-4935-TP'    'KRTAP4-9'     [17]    [ 39261809]    'C' 
    'GBM-76-4935-TP'    'ZNF814'       [19]    [ 58385546]    'T' 
    'GBM-76-6191-TP'    'MUC4'         [ 3]    [195515435]    'T' 
    'GBM-76-6192-TP'    'NBPF1'        [ 1]    [ 16918653]    'T' 
    'GBM-76-6280-TP'    'CNTNAP2'      [ 7]    [147183114]    'G' 
    'GBM-76-6282-TP'    'UGT2B10'      [ 4]    [ 69870669]    'A' 
    'GBM-76-6285-TP'    'NAB2'         [12]    [ 57485446]    'C' 
    'GBM-76-6286-TP'    'NBPF10'       [ 1]    [145367767]    'A' 
    'GBM-87-5896-TP'    'PRAMEF11'     [ 1]    [ 12885289]    'T' 
    'GBM-87-5896-TP'    'KRTAP4-11'    [17]    [ 39274291]    'C' 

Not enforcing any target list.
Collapsing adjacent mutations:
convert_chr: assuming human for chrX/chrY
Collapsed 21414 muts to 21414 muts
Getting context: 46% 93% 

Done.
Saved GBM-TP.mutation_preprocessing_report.txt
Saved GBM-TP.maf
Total of 291 patients had both MAF and WIG data.
Saved GBM-TP.patients.txt
Saved GBM-TP.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/285844
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 GBM-TP -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/GBM-TP/2283735/maf1.input.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM-TP/2283735/wig1.input.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0_cga.pancan.blacklist.v7.hg19.params.txt
