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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
BLCA
-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/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis6171327325170057654.att_MutSigPreprocess1.maf1.input.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis7922521579089203589.att_MutSigPreprocess1.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/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BL-A0C8-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BL-A13I-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BL-A13J-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A0S7-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A0YX-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20J-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20N-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20O-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20P-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20Q-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20T-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20U-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20V-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-BT-A20W-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-C4-A0EZ-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-C4-A0F0-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-C4-A0F1-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-C4-A0F6-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-C4-A0F7-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-CF-A1HR-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-CF-A1HS-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-CU-A0YN-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-CU-A0YO-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-CU-A0YR-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-DK-A1A3-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-DK-A1A5-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-DK-A1A7-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/blca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_BLCA.IlluminaGA_DNASeq.Level_2.2.2.0/TCGA-DK-A1AB-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [28]
                                BAM_file: [28]
      CCLE_ONCOMAP_overlapping_mutations: [28]
    CCLE_ONCOMAP_total_mutations_in_gene: [28]
                       CGC_Mutation_Type: [28]
                      CGC_Other_Diseases: [28]
               CGC_Translocation_Partner: [28]
                CGC_Tumor_Types_Germline: [28]
                 CGC_Tumor_Types_Somatic: [28]
                     COSMIC_fusion_genes: [28]
            COSMIC_overlapping_mutations: [28]
            COSMIC_tissue_types_affected: [28]
        COSMIC_total_alterations_in_gene: [28]
                                  Center: [28]
                              Chromosome: [28]
                            Codon_Change: [28]
                     DNARepairGenes_Role: [28]
                             Description: [28]
                                DrugBank: [28]
                            End_position: [28]
                          Entrez_Gene_Id: [28]
        FamilialCancerDatabase_Syndromes: [28]
                   GO_Biological_Process: [28]
                   GO_Cellular_Component: [28]
                   GO_Molecular_Function: [28]
                           Genome_Change: [28]
                             Hugo_Symbol: [28]
                MUTSIG_Published_Results: [28]
                  Match_Norm_Seq_Allele1: [28]
                  Match_Norm_Seq_Allele2: [28]
           Match_Norm_Validation_Allele1: [28]
           Match_Norm_Validation_Allele2: [28]
             Matched_Norm_Sample_Barcode: [28]
                         Mutation_Status: [28]
                              NCBI_Build: [28]
                             OREGANNO_ID: [28]
                         OREGANNO_Values: [28]
                       Other_Transcripts: [28]
                          Protein_Change: [28]
                        Reference_Allele: [28]
                          Refseq_mRNA_Id: [28]
                          Refseq_prot_Id: [28]
                                   Score: [28]
                         Sequence_Source: [28]
                               Sequencer: [28]
                        Sequencing_Phase: [28]
                          Start_position: [28]
                                  Strand: [28]
                        SwissProt_acc_Id: [28]
                      SwissProt_entry_Id: [28]
           TCGAscape_Amplification_Peaks: [28]
                TCGAscape_Deletion_Peaks: [28]
                         Transcript_Exon: [28]
                     Transcript_Position: [28]
                       Transcript_Strand: [28]
                    Tumor_Sample_Barcode: [28]
                       Tumor_Seq_Allele1: [28]
                       Tumor_Seq_Allele2: [28]
                Tumor_Validation_Allele1: [28]
                Tumor_Validation_Allele2: [28]
          Tumorscape_Amplification_Peaks: [28]
               Tumorscape_Deletion_Peaks: [28]
                           UniProt_AApos: [28]
               UniProt_Experimental_Info: [28]
              UniProt_Natural_Variations: [28]
                          UniProt_Region: [28]
                            UniProt_Site: [28]
                       Validation_Method: [28]
                       Validation_Status: [28]
                  Variant_Classification: [28]
                            Variant_Type: [28]
                     Verification_Status: [28]
                             cDNA_Change: [28]
                                 dataset: [28]
                                dbSNP_RS: [28]
                        dbSNP_Val_Status: [28]
                                  filter: [28]
                              gc_content: [28]
                                 patient: [28]
                             ref_context: [28]
                             t_alt_count: [28]
                             t_ref_count: [28]
                   validation_alt_allele: [28]
                       validation_method: [28]
                       validation_status: [28]
                 validation_tumor_sample: [28]
                               ----TOTAL: [2408]
Calling preprocess_mutations...
WARNING: unknown chromosome(s):
    'M'

Validation_Status:

             : [10380]
    ----TOTAL: [10380]
Omitting the following 4 mutations on nonstandard chromosomes:

            M: [4]
    ----TOTAL: [4]
Removing the following non-coding mutations (based on "type" field):
        3'UTR: [534]
      5'Flank: [60]
        5'UTR: [253]
          IGR: [319]
       Intron: [1656]
          RNA: [154]
    ----TOTAL: [2976]
Not enforcing any target list.
Collapsing adjacent mutations:
convert_chr: assuming human for chrX/chrY

    2 SNPs to one DNP (guessing "Missense"): [41]
                                  ----TOTAL: [41]

Genes affected:
        ASTN1: [1]
         CD27: [1]
         CDH8: [1]
       CELSR3: [1]
       CORO2B: [1]
       CRYBB1: [1]
          FGA: [1]
          FLG: [1]
      FOXRED2: [1]
        GANAB: [1]
       GXYLT2: [1]
        HERC2: [1]
       INPP4B: [1]
        ITIH5: [1]
        MECOM: [1]
        MIER1: [1]
       MIPOL1: [1]
        MYO5B: [1]
        NTRK1: [1]
        NXPH2: [1]
        OPCML: [1]
       OR51A7: [1]
        OR6K2: [1]
         OXR1: [1]
        PKHD1: [1]
         PLP2: [1]
       PRPF31: [1]
    RPL23AP32: [1]
        S1PR1: [1]
         SIM1: [1]
      SLC20A1: [1]
      SLC26A9: [1]
         ST7L: [1]
         TP53: [1]
      Unknown: [1]
        VASH1: [1]
        ZFP57: [1]
       ZNF283: [1]
       ZNF317: [1]
     C6orf222: [2]
    ----TOTAL: [41]

Patients affected:
    BLCA-BL-A13I: [1]
    BLCA-BL-A13J: [1]
    BLCA-BT-A0S7: [1]
    BLCA-BT-A20T: [1]
    BLCA-BT-A20U: [1]
    BLCA-C4-A0EZ: [1]
    BLCA-C4-A0F1: [1]
    BLCA-BT-A0YX: [2]
    BLCA-CF-A1HS: [2]
    BLCA-BT-A20J: [3]
    BLCA-BT-A20O: [4]
    BLCA-CU-A0YN: [4]
    BLCA-CU-A0YR: [4]
    BLCA-DK-A1A3: [5]
    BLCA-BT-A20N: [10]
       ----TOTAL: [41]
convert_chr: assuming human for chrX/chrY
Collapsed 7400 muts to 7359 muts
Getting context: 
Done.
Saved BLCA.mutation_preprocessing_report.txt
Saved BLCA.maf
Total of 28 patients had both MAF and WIG data.
Saved BLCA.patients.txt
Saved BLCA.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/159945
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 BLCA -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/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis6171327325170057654.att_MutSigPreprocess1.maf1.input.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis7922521579089203589.att_MutSigPreprocess1.wig1.input.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
