2016-08-19 15:05:18,315 INFO [oncotator.Oncotator:239] Oncotator v1.9.0.0 2016-08-19 15:05:18,315 INFO [oncotator.Oncotator:240] Args: Namespace(allow_overwriting=False, cache_url=None, canonical_tx_file=None, collapse_filter_cols=False, collapse_number_annotations=False, dbDir='/xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', infer_onps=False, input_file='/fh/subscription-garraway_lab/GermlinePipelineSubsetVCFSingleSample/CANSEQU01-0400067-TP-NB-SM-AJDYI-SM-AJDZB/26058471/SM-AJDZB.GATK_PrimitiveAlleles.vcf.gz', input_format='VCF', log_name='oncotator.log', noMulticore=False, output_file='CANSEQU01-0400067-Normal-SM-AJDZB.maf', output_format='TCGAMAF', override_cli=[], override_config='/xchip/cga/reference/annotation/db/tcgaMAFManualOverrides2.4.config', prepend=False, read_only_cache=False, reannotate_tcga_maf_cols=False, skip_no_alt=True, tx_mode='EFFECT', verbose=6) 2016-08-19 15:05:18,316 INFO [oncotator.Oncotator:241] Log file: /fh/subscription-garraway_lab/VCF2MAF/CANSEQU01-0400067-TP-NB-SM-AJDYI-SM-AJDZB/26076340/oncotator.log 2016-08-19 15:05:18,342 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cosmic_fusion/hg19/cosmic_fusion.config 2016-08-19 15:05:18,343 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/gencode_xrefseq/hg19/gencode_xrefseq.config 2016-08-19 15:05:18,344 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/clinvar/hg19/clinvar.config 2016-08-19 15:05:18,345 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/exac/hg19/exac.config 2016-08-19 15:05:18,347 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ccle_by_gene/hg19/ccle_by_gene.config 2016-08-19 15:05:18,348 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/oreganno/hg19/oreganno.config 2016-08-19 15:05:18,349 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/achilles/hg19/achilles.config 2016-08-19 15:05:18,351 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cancer_gene_census/hg19/cancer_gene_census.config 2016-08-19 15:05:18,352 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/simple_uniprot/hg19/simple_uniprot.config 2016-08-19 15:05:18,354 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/dna_repair_genes/hg19/dna_repair_genes.config 2016-08-19 15:05:18,361 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/dbsnp/hg19/dbsnp.config 2016-08-19 15:05:18,369 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ref_hg/hg19/ref_hg.config 2016-08-19 15:05:18,370 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/uniprot_aa_xform/hg19/uniprot_aa_xform.config 2016-08-19 15:05:18,371 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/gencode_out2/hg19/gencode_out2.config 2016-08-19 15:05:18,373 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/hgnc/hg19/hgnc.config 2016-08-19 15:05:18,374 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ccle_by_gp/hg19/ccle_by_gp.config 2016-08-19 15:05:18,376 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cosmic_tissue/hg19/cosmic_tissue.config 2016-08-19 15:05:18,378 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/familial/hg19/familial.config 2016-08-19 15:05:18,379 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/tumorscape/hg19/tumorscape.config 2016-08-19 15:05:18,380 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cosmic/hg19/cosmic.config 2016-08-19 15:05:18,382 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/1000genome_db/hg19/1000genome_db.config 2016-08-19 15:05:18,384 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/uniprot_aa_annotation/hg19/uniprot_aa_annotation.config 2016-08-19 15:05:18,385 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/dbNSFP_ds/hg19/dbNSFP_ds.config 2016-08-19 15:05:18,386 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/so_terms/hg19/so_terms.config 2016-08-19 15:05:18,388 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/tcgascape/hg19/tcgascape.config 2016-08-19 15:05:18,390 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/mutsig/hg19/mutsig.config 2016-08-19 15:05:18,391 INFO [oncotator.DatasourceFactory:304] Creating pool 2016-08-19 15:05:18,423 INFO [oncotator.DatasourceFactory:307] Pool created 2016-08-19 15:05:18,773 INFO [oncotator.datasources.EnsemblTranscriptDatasource:95] GENCODE v19 is being set up in faster, NOT thread-safe mode (for annotation). 2016-08-19 15:05:19,120 INFO [oncotator.datasources.EnsemblTranscriptDatasource:106] GENCODE v19 is being set up with default tx-mode: CANONICAL. 2016-08-19 15:05:19,121 WARNING [oncotator.datasources.EnsemblTranscriptDatasource:123] Attempting to set transcript mode of CANONICAL for ensembl. This operation is only supported for GENCODE. Otherwise, will be the same as EFFECT. 2016-08-19 15:05:19,121 INFO [oncotator.datasources.EnsemblTranscriptDatasource:109] GENCODE v19 is being set up with basic filtering. 2016-08-19 15:05:19,503 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/so_terms/hg19//SO_Ensembl_consequence_terms.bin... 2016-08-19 15:05:19,537 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cosmic_fusion/hg19//CosmicFusionExport.v76.bin... 2016-08-19 15:05:19,542 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/clinvar/hg19//clinvar_hgmd.12-03-20.bin... 2016-08-19 15:05:19,545 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/oreganno/hg19//oreganno_results_by_pos.hg19.import.bin... 2016-08-19 15:05:19,546 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cancer_gene_census/hg19//CancerGeneCensus_Table_1_full_2012-03-15.bin... 2016-08-19 15:05:19,607 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/gencode_xrefseq/hg19//gencode_xrefseq_v19.bin... 2016-08-19 15:05:19,674 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/simple_uniprot/hg19//simple_uniprot_Dec012014.bin... 2016-08-19 15:05:20,449 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/achilles/hg19//achilles_lineage_results.import.bin... 2016-08-19 15:05:20,847 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/dna_repair_genes/hg19//Wood_DNARepairGenes.no_dupes.bin... 2016-08-19 15:05:20,859 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/hgnc/hg19//hgnc_download_Sept172014.bin... 2016-08-19 15:05:21,337 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ccle_by_gp/hg19//ccle_results_by_pos.hg19.import.bin... 2016-08-19 15:05:21,364 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/cosmic_tissue/hg19//CosmicCompleteTargetedScreensMutantExport.v76.geneHistology.bin... 2016-08-19 15:05:21,784 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/familial/hg19//Familial Cancer Genes.no_dupes.bin... 2016-08-19 15:05:21,809 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/tumorscape/hg19//tumorscape_20100104_generated.bin... 2016-08-19 15:05:22,430 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/uniprot_aa_annotation/hg19//uniprot_aa_annotations.bin... 2016-08-19 15:05:22,669 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/mutsig/hg19//mutsig_results.import.20110905.bin... 2016-08-19 15:05:22,733 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ccle_by_gene/hg19//ccle_results_by_gene.import.bin... 2016-08-19 15:05:30,060 INFO [root:73] Loading /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/tcgascape/hg19//tcgascape_110405_generated.bin... 2016-08-19 15:05:39,078 INFO [oncotator.DatasourceFactory:321] Mapping complete: 17 datasources created in multiprocess 2016-08-19 15:05:39,503 INFO [oncotator.utils.RunSpecificationFactory:124] Setting GENCODE v19 to tx-mode of EFFECT... 2016-08-19 15:05:39,504 INFO [oncotator.utils.RunSpecificationFactory:135] No custom canonical transcripts specified. 2016-08-19 15:05:39,560 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (tcgaMAF2.4_output.config). Trying configs/ prepend. 2016-08-19 15:05:39,573 INFO [oncotator.output.TcgaMafOutputRenderer:93] Building alternative keys dictionary... 2016-08-19 15:05:39,620 INFO [oncotator.cache.DummyCache:57] No cache specified. All cache attempts will be listed as cache misses. 2016-08-19 15:05:39,620 INFO [oncotator.Annotator:426] Annotating with 26 datasources: Oncotator v1.9.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ExAC 0.3.1 | dbSNP build 142 | COSMIC v76 | 1000gp3 20130502 | dbNSFP v2.4 | ClinVar 12.03.20 | ORegAnno UCSC Track | CCLE_By_GP 09292010 | UniProt_AA 2014_12 | Ensembl ICGC MUCOPA | COSMIC_FusionGenes v76 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue v76 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | TCGAScape 110405 | MutSig Published Results 20110905 2016-08-19 15:05:39,623 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2016-08-19 15:05:39,681 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: CANSEQU01-0400067-Normal-SM-AJDZB.maf 2016-08-19 15:05:39,682 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting... 2016-08-19 15:05:39,682 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2016-08-19 15:05:40,356 WARNING [oncotator.output.TcgaMafOutputRenderer:219] Entrez Gene ID was zero, but Hugo Symbol was not Unknown. Is the HGNC and/or Transcript datasource complete? 2016-08-19 15:07:06,844 INFO [oncotator.output.TcgaMafOutputRenderer:330] Rendered 1000 mutations. 2016-08-19 15:07:54,291 ERROR [oncotator.output.TcgaMafOutputRenderer:333] Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 321, in renderMutations for m in mutations: File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 448, in _applyManualAnnotations for m in mutations: File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 456, in _applyDefaultAnnotations for m in mutations: File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 519, in _annotate_mutations_using_datasources m = self._annotate_func_ptr(m, datasource) File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 88, in _annotate_mut return ds.annotate_mutation(m) File "build/bdist.linux-x86_64/egg/oncotator/datasources/EnsemblTranscriptDatasource.py", line 206, in annotate_mutation ref_allele=mutation.ref_allele, alt_allele=mutation.alt_allele, start=mutation.start, end=mutation.end) File "build/bdist.linux-x86_64/egg/oncotator/utils/VariantClassifier.py", line 445, in variant_classify return self._determine_vc_for_cds_overlap(start, end, ref_allele, alt_allele, is_frameshift_indel, is_splice_site, tx, variant_type, is_start_codon_overlap) File "build/bdist.linux-x86_64/egg/oncotator/utils/VariantClassifier.py", line 313, in _determine_vc_for_cds_overlap observed_aa = MutUtils.translate_sequence(mutated_codon_seq) File "build/bdist.linux-x86_64/egg/oncotator/utils/MutUtils.py", line 460, in translate_sequence output_seq = Seq.translate(input_seq) File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/Bio/Seq.py", line 2149, in translate return _translate_str(sequence, codon_table, stop_symbol, to_stop, cds) File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/Bio/Seq.py", line 2060, in _translate_str "Codon '{0}' is invalid".format(codon)) TranslationError: Codon 'TC*' is invalid 2016-08-19 15:07:54,293 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 1608 ['1', 152129066, 152129101, 'TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA', '-']: 2016-08-19 15:07:54,293 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 1608 mutations. Traceback (most recent call last): File "/xchip/tcga/Tools/oncotator/onco_env/ubin/oncotator", line 9, in load_entry_point('Oncotator==1.9.0.0', 'console_scripts', 'oncotator')() File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 309, in main File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 437, in annotate File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 337, in renderMutations Bio.Data.CodonTable.TranslationError: Codon 'TC*' is invalid