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fh_MutSigPreprocess
-i
CESC
-b
hg19
-t
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
-c
/xchip/cga1/annotation/db/tracks/hg19/c65e
-cw
no_longer_needed
-cat
4
-maf1
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis9093673244185788920.att_dependentsValues1266616200307118267.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/Axis7332586965858239789.att_dependentsValues6816902004021326039.tsv
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt

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

Loading MAFs for Broad
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VR-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VS-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A0TN-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BE-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BF-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BI-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BJ-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BK-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BL-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BM-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BN-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M5-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M6-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M7-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M8-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M9-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ME-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MF-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MH-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MI-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MJ-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MK-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ML-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MN-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MP-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MQ-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZL-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZM-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VK-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VL-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VM-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VN-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EA-A1QT-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EX-A1H5-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23K-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23L-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [36]
                                BAM_file: [36]
      CCLE_ONCOMAP_overlapping_mutations: [36]
    CCLE_ONCOMAP_total_mutations_in_gene: [36]
                       CGC_Mutation_Type: [36]
                      CGC_Other_Diseases: [36]
               CGC_Translocation_Partner: [36]
                CGC_Tumor_Types_Germline: [36]
                 CGC_Tumor_Types_Somatic: [36]
                     COSMIC_fusion_genes: [36]
            COSMIC_overlapping_mutations: [36]
            COSMIC_tissue_types_affected: [36]
        COSMIC_total_alterations_in_gene: [36]
                                  Center: [36]
                              Chromosome: [36]
                            Codon_Change: [36]
                     DNARepairGenes_Role: [36]
                             Description: [36]
                                DrugBank: [36]
                            End_position: [36]
                          Entrez_Gene_Id: [36]
        FamilialCancerDatabase_Syndromes: [36]
                   GO_Biological_Process: [36]
                   GO_Cellular_Component: [36]
                   GO_Molecular_Function: [36]
                           Genome_Change: [36]
                             Hugo_Symbol: [36]
                MUTSIG_Published_Results: [36]
                  Match_Norm_Seq_Allele1: [36]
                  Match_Norm_Seq_Allele2: [36]
           Match_Norm_Validation_Allele1: [36]
           Match_Norm_Validation_Allele2: [36]
             Matched_Norm_Sample_Barcode: [36]
                         Mutation_Status: [36]
                              NCBI_Build: [36]
                             OREGANNO_ID: [36]
                         OREGANNO_Values: [36]
                       Other_Transcripts: [36]
                          Protein_Change: [36]
                        Reference_Allele: [36]
                          Refseq_mRNA_Id: [36]
                          Refseq_prot_Id: [36]
                                   Score: [36]
                         Sequence_Source: [36]
                               Sequencer: [36]
                        Sequencing_Phase: [36]
                          Start_position: [36]
                                  Strand: [36]
                        SwissProt_acc_Id: [36]
                      SwissProt_entry_Id: [36]
           TCGAscape_Amplification_Peaks: [36]
                TCGAscape_Deletion_Peaks: [36]
                         Transcript_Exon: [36]
                     Transcript_Position: [36]
                       Transcript_Strand: [36]
                    Tumor_Sample_Barcode: [36]
                       Tumor_Seq_Allele1: [36]
                       Tumor_Seq_Allele2: [36]
                Tumor_Validation_Allele1: [36]
                Tumor_Validation_Allele2: [36]
          Tumorscape_Amplification_Peaks: [36]
               Tumorscape_Deletion_Peaks: [36]
                           UniProt_AApos: [36]
               UniProt_Experimental_Info: [36]
              UniProt_Natural_Variations: [36]
                          UniProt_Region: [36]
                            UniProt_Site: [36]
                       Validation_Method: [36]
                       Validation_Status: [36]
                  Variant_Classification: [36]
                            Variant_Type: [36]
                     Verification_Status: [36]
                             cDNA_Change: [36]
                                 dataset: [36]
                                dbSNP_RS: [36]
                        dbSNP_Val_Status: [36]
                                  filter: [36]
                              gc_content: [36]
                                 patient: [36]
                             ref_context: [36]
                             t_alt_count: [36]
                             t_ref_count: [36]
                   validation_alt_allele: [36]
                       validation_method: [36]
                       validation_status: [36]
                 validation_tumor_sample: [36]
                               ----TOTAL: [3096]
Calling preprocess_mutations...
Validation_Status:

             : [9967]
    ----TOTAL: [9967]
Removing the following non-coding mutations (based on "type" field):
        3'UTR: [105]
      5'Flank: [57]
        5'UTR: [60]
          IGR: [325]
       Intron: [2088]
          RNA: [46]
    ----TOTAL: [2681]
Not enforcing any target list.
Collapsing adjacent mutations:

    2 SNPs to one DNP (guessing "Missense"): [15]
                                  ----TOTAL: [15]

Genes affected:
       BARHL2: [1]
      CCDC85A: [1]
        CHEK2: [1]
        COASY: [1]
         DPP9: [1]
       ELMOD2: [1]
        ESRP2: [1]
       GABRG1: [1]
        KCNA1: [1]
        KIFC1: [1]
         MYH1: [1]
     PLEKHG4B: [1]
        QPCTL: [1]
       RHOXF1: [1]
       ZNF773: [1]
    ----TOTAL: [15]

Patients affected:
    CESC-C5-A1BJ: [1]
    CESC-C5-A1M7: [1]
    CESC-C5-A1M8: [1]
    CESC-C5-A1MJ: [1]
    CESC-C5-A1MK: [1]
    CESC-C5-A1MN: [1]
    CESC-DS-A0VK: [1]
    CESC-DS-A0VM: [1]
    CESC-C5-A1ML: [2]
    CESC-FU-A23K: [2]
    CESC-DR-A0ZM: [3]
       ----TOTAL: [15]
Collapsed 7286 muts to 7271 muts
Getting context: 
Done.
Saved CESC.mutation_preprocessing_report.txt
Saved CESC.maf
Total of 36 patients had both MAF and WIG data.
Saved CESC.patients.txt
Saved CESC.coverage.prepare.txt
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142821
mFile: fh_MutSigPreprocess
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/fh_MutSigPreprocess -i CESC -b hg19 -t /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt -c /xchip/cga1/annotation/db/tracks/hg19/c65e -cw no_longer_needed -cat 4 -maf1 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis9093673244185788920.att_dependentsValues1266616200307118267.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/Axis7332586965858239789.att_dependentsValues6816902004021326039.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
