Class org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
tests
failures
ignored
1m44.37s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
exhaustiveArgumentTest[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null)	1.135s	passed
exhaustiveArgumentTest[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null)	1.146s	passed
exhaustiveArgumentTest[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null)	1.090s	passed
exhaustiveArgumentTest[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null)	1.131s	passed
exhaustiveArgumentTest[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null)	1.126s	passed
exhaustiveArgumentTest[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null)	1.126s	passed
exhaustiveArgumentTest[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null)	0.941s	passed
exhaustiveArgumentTest[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null)	1.025s	passed
metaTestEnsureTempDirs	0s	passed
nonTrivialLargeDataValidationTest[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, [], false)	6.395s	passed
nonTrivialLargeDataValidationTest[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf, [], false)	5.722s	passed
nonTrivialLargeDataValidationTest[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false)	1.946s	passed
nonTrivialLargeDataValidationTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, hg38, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf, [], false)	2.139s	passed
nonTrivialLargeDataValidationTest[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf, [], true)	12.951s	passed
testAlreadyAnnotatedInputWithOverrideArgument[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf)	6.048s	passed
testAlreadyAnnotatedInputWithoutOverrideArgument[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf)	0.076s	passed
testCanAnnotateHg38ClinvarAndGencodeV28	0.192s	passed
testCanAnnotateMixedContigHg19Clinvar	0.099s	passed
testCanAnnotateSpanningDeletions	0.193s	passed
testCanCreateNonLocatableFuncotations	0.973s	passed
testCanHandleSymbollicAlleleFuncotations	1.004s	passed
testCustomVariantClassificationOrder	0.964s	passed
testEColiFuncotations	0.099s	passed
testEnsureDbSnpInMaf	0.077s	passed
testExclusionFromDatasourceVcfToVcf	0.176s	passed
testFilterParsing	0.112s	passed
testFuncotatorWithoutValidatingResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null)	0.985s	passed
testFuncotatorWithoutValidatingResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null)	1.027s	passed
testFuncotatorWithoutValidatingResults[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null)	1.009s	passed
testFuncotatorWithoutValidatingResults[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null)	1.138s	passed
testFuncotatorWithoutValidatingResults[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null)	1.015s	passed
testFuncotatorWithoutValidatingResults[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null)	1.130s	passed
testFuncotatorWithoutValidatingResults[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder7089501280763091247/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null)	1.000s	passed
testFuncotatorWithoutValidatingResults[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null)	1.082s	passed
testMANESelectAnnotationDifferencesAndGencodeV43	0.320s	passed
testMafCustomCountFieldsTumorOnly[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf)	0.080s	passed
testMafCustomCountFieldsTumorOnly[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf)	0.077s	passed
testMafCustomCountFields[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf)	0.080s	passed
testMafCustomCountFields[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf)	0.077s	passed
testManualAnnotationsCorrectness	0.089s	passed
testMoreThanOneTNPair	0.071s	passed
testNoSpanningDeletionWriteWithMAF	0.124s	passed
testNoVariantsProduceMaf	0.070s	passed
testSequenceDictionaryCheck	0.065s	passed
testUnannotatedInputWithOverrideArgument[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf)	6.156s	passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput	0.851s	passed
testVCFColumnsArentShuffled	0.080s	passed
testVCFToMAFPreservesFields	0.086s	passed
testVCFToVCFPreservesFields	0.094s	passed
testVcfDatasourceAccountsForAltAlleles	0.081s	passed
testVcfMafConcordance[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder1664273143089301610/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15)	0.168s	passed
testVcfMafConcordance[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder1664273143089301610/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.215s	passed
testVcfMafConcordance[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder15667030383423959625/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057)	38.402s	passed
testVcfMafConcordance[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder12440037073314555051/hg38.3.fasta, hg38, [Gencode_28_hugoSymbol, Gencode_28_ncbiBuild, Gencode_28_chromosome, Gencode_28_start, Gencode_28_end, Gencode_28_variantClassification, Gencode_28_variantType, Gencode_28_refAllele, Gencode_28_tumorSeqAllele1, Gencode_28_tumorSeqAllele2, Gencode_28_genomeChange, Gencode_28_annotationTranscript, Gencode_28_transcriptStrand, Gencode_28_transcriptExon, Gencode_28_transcriptPos, Gencode_28_cDnaChange, Gencode_28_codonChange, Gencode_28_proteinChange, Gencode_28_gcContent, Gencode_28_referenceContext, Gencode_28_otherTranscripts], [Hugo_Symbol, NCBI_Build, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Genome_Change, Annotation_Transcript, Transcript_Strand, Transcript_Exon, Transcript_Position, cDNA_Change, Codon_Change, Protein_Change, gc_content, ref_context, Other_Transcripts], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, false, 104)	0.364s	passed
testVcfMafConcordance[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder1664273143089301610/b37.3.fasta, hg19, [Gencode_19_hugoSymbol, Gencode_19_ncbiBuild, Gencode_19_chromosome, Gencode_19_start, Gencode_19_end, Gencode_19_variantClassification, Gencode_19_variantType, Gencode_19_refAllele, Gencode_19_tumorSeqAllele1, Gencode_19_tumorSeqAllele2, Gencode_19_genomeChange, Gencode_19_annotationTranscript, Gencode_19_transcriptStrand, Gencode_19_transcriptExon, Gencode_19_transcriptPos, Gencode_19_cDnaChange, Gencode_19_codonChange, Gencode_19_proteinChange, Gencode_19_gcContent, Gencode_19_referenceContext, Gencode_19_otherTranscripts], [Hugo_Symbol, NCBI_Build, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Genome_Change, Annotation_Transcript, Transcript_Strand, Transcript_Exon, Transcript_Position, cDNA_Change, Codon_Change, Protein_Change, gc_content, ref_context, Other_Transcripts], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.234s	passed
testVcfToMafHonorsExcludedFields	0.085s	passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified	0.109s	passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations	0.123s	passed
Standard error

18:10:44.921 INFO  Funcotator - ------------------------------------------------------------
18:10:44.921 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:44.921 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:44.921 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:44.921 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:44.921 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:44 PM UTC
18:10:44.921 INFO  Funcotator - ------------------------------------------------------------
18:10:44.921 INFO  Funcotator - ------------------------------------------------------------
18:10:44.921 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:44.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:44.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:44.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:44.921 INFO  Funcotator - Deflater: IntelDeflater
18:10:44.922 INFO  Funcotator - Inflater: IntelInflater
18:10:44.922 INFO  Funcotator - GCS max retries/reopens: 20
18:10:44.922 INFO  Funcotator - Requester pays: disabled
18:10:44.922 INFO  Funcotator - Initializing engine
18:10:44.923 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:10:44.924 INFO  Funcotator - Done initializing engine
18:10:44.924 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:44.924 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:44.924 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder10519034235316905828/TranscriptIdFile.txt
18:10:44.924 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
18:10:44.924 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:44.924 INFO  Funcotator - Initializing data sources...
18:10:44.924 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:44.924 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:44.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:44.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:44.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:44.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:44.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:44.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:44.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:44.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:44.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:44.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:44.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:44.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:44.928 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:44.928 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:44.928 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:44.928 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:44.929 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:45.012 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:45.055 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:45.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:45.082 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:45.082 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:45.083 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:45.083 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:45.719 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:45.757 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:45.757 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:45.758 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:45.758 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:45.856 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:45.857 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:45.858 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:45.885 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:45.886 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:45.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:45.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:45.888 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:45.888 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:45.888 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:45.891 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:45.894 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:45.896 INFO  Funcotator - Initializing Funcotator Engine...
18:10:45.896 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:45.896 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:10:45.896 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:10:45.897 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:10:45.897 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:10:45.898 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:10:45.899 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:10:45.900 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:10:45.900 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:10:45.900 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:45.900 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.310653345736954728930.vcf
18:10:45.900 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:45.903 INFO  ProgressMeter - Starting traversal
18:10:45.903 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:45.982 INFO  ProgressMeter -             unmapped              0.0                     3           2278.5
18:10:45.982 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:10:45.982 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:10:45.986 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2187329536
18:10:46.057 INFO  Funcotator - ------------------------------------------------------------
18:10:46.057 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:46.057 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:46.057 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:46.057 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:46.057 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:46 PM UTC
18:10:46.058 INFO  Funcotator - ------------------------------------------------------------
18:10:46.058 INFO  Funcotator - ------------------------------------------------------------
18:10:46.058 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:46.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:46.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:46.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:46.058 INFO  Funcotator - Deflater: IntelDeflater
18:10:46.058 INFO  Funcotator - Inflater: IntelInflater
18:10:46.058 INFO  Funcotator - GCS max retries/reopens: 20
18:10:46.058 INFO  Funcotator - Requester pays: disabled
18:10:46.058 INFO  Funcotator - Initializing engine
18:10:46.059 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:10:46.060 INFO  Funcotator - Done initializing engine
18:10:46.060 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:46.060 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:46.060 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder11582751228485137712/TranscriptIdFile.txt
18:10:46.060 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
18:10:46.060 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:46.060 INFO  Funcotator - Initializing data sources...
18:10:46.061 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:46.061 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:46.061 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:46.061 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:46.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:46.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:46.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:46.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:46.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:46.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:46.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:46.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:46.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:46.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:46.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:46.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:46.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:46.064 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:46.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:46.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:46.108 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:46.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:46.135 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:46.135 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:46.136 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:46.136 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:46.747 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:46.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:46.830 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:46.831 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:46.831 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:46.915 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:46.916 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:46.916 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:46.943 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:46.944 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:46.944 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:46.944 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:46.945 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:46.945 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:46.946 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:46.948 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:46.951 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:46.953 INFO  Funcotator - Initializing Funcotator Engine...
18:10:46.953 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:10:46.953 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:46.953 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.416795640231195501586.vcf
18:10:46.954 INFO  ProgressMeter - Starting traversal
18:10:46.954 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:47.132 INFO  ProgressMeter -             unmapped              0.0                     4           1348.3
18:10:47.132 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:10:47.132 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:10:47.132 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2187329536
18:10:47.200 INFO  Funcotator - ------------------------------------------------------------
18:10:47.200 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:47.200 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:47.200 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:47.200 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:47.200 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:47 PM UTC
18:10:47.200 INFO  Funcotator - ------------------------------------------------------------
18:10:47.200 INFO  Funcotator - ------------------------------------------------------------
18:10:47.200 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:47.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:47.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:47.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:47.200 INFO  Funcotator - Deflater: IntelDeflater
18:10:47.200 INFO  Funcotator - Inflater: IntelInflater
18:10:47.200 INFO  Funcotator - GCS max retries/reopens: 20
18:10:47.200 INFO  Funcotator - Requester pays: disabled
18:10:47.201 INFO  Funcotator - Initializing engine
18:10:47.201 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:10:47.202 INFO  Funcotator - Done initializing engine
18:10:47.202 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:47.202 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:47.202 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder5024582240742175030/TranscriptIdFile.txt
18:10:47.202 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
18:10:47.202 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:47.202 INFO  Funcotator - Initializing data sources...
18:10:47.202 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:47.202 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:47.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:47.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:47.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:47.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:47.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:47.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:47.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:47.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:47.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:47.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:47.205 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:47.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:47.206 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:47.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:47.268 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:47.276 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:47.276 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:47.277 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:47.277 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:47.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:48.033 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:48.033 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:48.034 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:48.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:48.117 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:48.117 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:48.118 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:48.145 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:48.145 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:48.146 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:48.178 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:48.178 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:48.178 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:48.179 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:48.181 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:48.184 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:48.186 INFO  Funcotator - Initializing Funcotator Engine...
18:10:48.186 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:48.187 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:10:48.187 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:10:48.187 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:10:48.187 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:10:48.188 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:10:48.188 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:48.188 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.3350598356912481901.vcf
18:10:48.189 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:48.190 INFO  ProgressMeter - Starting traversal
18:10:48.190 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:48.219 INFO  ProgressMeter -             unmapped              0.0                     3           6206.9
18:10:48.219 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:10:48.220 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:10:48.223 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:48 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2384461824
18:10:48.293 INFO  Funcotator - ------------------------------------------------------------
18:10:48.293 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:48.293 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:48.293 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:48.293 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:48.293 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:48 PM UTC
18:10:48.293 INFO  Funcotator - ------------------------------------------------------------
18:10:48.293 INFO  Funcotator - ------------------------------------------------------------
18:10:48.293 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:48.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:48.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:48.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:48.293 INFO  Funcotator - Deflater: IntelDeflater
18:10:48.293 INFO  Funcotator - Inflater: IntelInflater
18:10:48.293 INFO  Funcotator - GCS max retries/reopens: 20
18:10:48.293 INFO  Funcotator - Requester pays: disabled
18:10:48.293 INFO  Funcotator - Initializing engine
18:10:48.294 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:10:48.295 INFO  Funcotator - Done initializing engine
18:10:48.295 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:48.295 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:48.295 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder15146661751070792421/TranscriptIdFile.txt
18:10:48.295 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
18:10:48.295 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:48.295 INFO  Funcotator - Initializing data sources...
18:10:48.295 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:48.295 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:48.295 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:48.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:48.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:48.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:48.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:48.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:48.297 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:48.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:48.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:48.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:48.298 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:48.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:48.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:48.341 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:48.360 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:48.367 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:48.367 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:48.367 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:48.368 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:49.028 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:49.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:49.065 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:49.066 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:49.066 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:49.176 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:49.176 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:49.177 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:49.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:49.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:49.204 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:49.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:49.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:49.205 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:49.206 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:49.208 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:49.213 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:49.216 INFO  Funcotator - Initializing Funcotator Engine...
18:10:49.216 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:10:49.216 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:49.216 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.46907517701535697130.vcf
18:10:49.218 INFO  ProgressMeter - Starting traversal
18:10:49.218 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:49.353 INFO  ProgressMeter -             unmapped              0.0                     4           1777.8
18:10:49.353 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:10:49.353 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:10:49.353 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2514485248
18:10:49.420 INFO  Funcotator - ------------------------------------------------------------
18:10:49.420 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:49.420 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:49.420 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:49.420 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:49.420 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:49 PM UTC
18:10:49.420 INFO  Funcotator - ------------------------------------------------------------
18:10:49.420 INFO  Funcotator - ------------------------------------------------------------
18:10:49.420 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:49.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:49.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:49.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:49.420 INFO  Funcotator - Deflater: IntelDeflater
18:10:49.420 INFO  Funcotator - Inflater: IntelInflater
18:10:49.420 INFO  Funcotator - GCS max retries/reopens: 20
18:10:49.420 INFO  Funcotator - Requester pays: disabled
18:10:49.420 INFO  Funcotator - Initializing engine
18:10:49.421 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:10:49.422 INFO  Funcotator - Done initializing engine
18:10:49.422 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:49.422 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:49.422 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6106861049202869518/TranscriptIdFile.txt
18:10:49.422 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
18:10:49.422 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:49.422 INFO  Funcotator - Initializing data sources...
18:10:49.422 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:49.422 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:49.422 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:49.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:49.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:49.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:49.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:49.425 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:49.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:49.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:49.468 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:49.486 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:49.493 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:49.494 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:49.494 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:49.494 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:50.220 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:50.274 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:50.274 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:50.275 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:50.275 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:50.378 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:50.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:50.379 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:50.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:50.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:50.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:50.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:50.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:50.412 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:50.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:50.417 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:50.421 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:50.425 INFO  Funcotator - Initializing Funcotator Engine...
18:10:50.425 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:50.425 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:10:50.425 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:10:50.425 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:10:50.425 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:10:50.426 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:10:50.426 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:50.426 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.32282921184145629185.maf
18:10:50.429 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:10:50.431 INFO  ProgressMeter - Starting traversal
18:10:50.431 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:50.479 INFO  ProgressMeter -             unmapped              0.0                     3           3750.0
18:10:50.479 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:10:50.480 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:10:50.480 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2915041280
18:10:50.550 INFO  Funcotator - ------------------------------------------------------------
18:10:50.550 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:50.550 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:50.551 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:50.551 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:50.551 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:50 PM UTC
18:10:50.551 INFO  Funcotator - ------------------------------------------------------------
18:10:50.551 INFO  Funcotator - ------------------------------------------------------------
18:10:50.551 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:50.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:50.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:50.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:50.551 INFO  Funcotator - Deflater: IntelDeflater
18:10:50.551 INFO  Funcotator - Inflater: IntelInflater
18:10:50.551 INFO  Funcotator - GCS max retries/reopens: 20
18:10:50.551 INFO  Funcotator - Requester pays: disabled
18:10:50.551 INFO  Funcotator - Initializing engine
18:10:50.552 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:10:50.553 INFO  Funcotator - Done initializing engine
18:10:50.553 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:50.553 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:50.553 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder11870599919624795391/TranscriptIdFile.txt
18:10:50.553 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
18:10:50.553 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:50.553 INFO  Funcotator - Initializing data sources...
18:10:50.554 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:50.554 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:50.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:50.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:50.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:50.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:50.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:50.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:50.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:50.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:50.557 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:50.557 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:50.557 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:50.557 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:50.557 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:50.640 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:50.679 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:50.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:50.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:50.693 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:50.693 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:51.247 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:51.361 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:51.361 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:51.362 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:51.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:51.445 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:51.446 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:51.446 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:51.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:51.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:51.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:51.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:51.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:51.475 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:51.476 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:51.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:51.481 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:51.483 INFO  Funcotator - Initializing Funcotator Engine...
18:10:51.483 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:10:51.483 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:51.483 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.414665364381234824830.maf
18:10:51.484 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:10:51.485 INFO  ProgressMeter - Starting traversal
18:10:51.485 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:51.605 INFO  ProgressMeter -             unmapped              0.0                     4           2000.0
18:10:51.605 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:10:51.606 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:10:51.606 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2915041280
18:10:51.673 INFO  Funcotator - ------------------------------------------------------------
18:10:51.673 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:51.673 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:51.673 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:51.673 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:51.673 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:51 PM UTC
18:10:51.673 INFO  Funcotator - ------------------------------------------------------------
18:10:51.673 INFO  Funcotator - ------------------------------------------------------------
18:10:51.673 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:51.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:51.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:51.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:51.673 INFO  Funcotator - Deflater: IntelDeflater
18:10:51.673 INFO  Funcotator - Inflater: IntelInflater
18:10:51.673 INFO  Funcotator - GCS max retries/reopens: 20
18:10:51.673 INFO  Funcotator - Requester pays: disabled
18:10:51.673 INFO  Funcotator - Initializing engine
18:10:51.674 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:10:51.675 INFO  Funcotator - Done initializing engine
18:10:51.675 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:51.675 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:51.675 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder5368402854279811842/TranscriptIdFile.txt
18:10:51.675 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
18:10:51.675 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:51.675 INFO  Funcotator - Initializing data sources...
18:10:51.675 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:51.675 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:51.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:51.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:51.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:51.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:51.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:51.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:51.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:51.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:51.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:51.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:51.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:51.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:51.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:51.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:51.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:51.678 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:51.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:51.679 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:51.725 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:51.744 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:51.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:51.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:51.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:51.752 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:52.353 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:52.391 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:52.391 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:52.392 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:52.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:52.474 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:52.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:52.475 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:52.502 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:52.502 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:52.503 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:52.503 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:52.503 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:52.503 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:52.504 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:52.507 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:52.511 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:52.514 INFO  Funcotator - Initializing Funcotator Engine...
18:10:52.515 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:10:52.515 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:10:52.515 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:10:52.515 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:10:52.515 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:10:52.516 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:10:52.516 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:52.516 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.311498326426074573914.maf
18:10:52.516 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:10:52.518 INFO  ProgressMeter - Starting traversal
18:10:52.518 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:52.546 INFO  ProgressMeter -             unmapped              0.0                     3           6428.6
18:10:52.546 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:10:52.546 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:10:52.546 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2915041280
18:10:52.614 INFO  Funcotator - ------------------------------------------------------------
18:10:52.614 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:52.614 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:52.614 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:52.614 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:52.614 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:52 PM UTC
18:10:52.614 INFO  Funcotator - ------------------------------------------------------------
18:10:52.614 INFO  Funcotator - ------------------------------------------------------------
18:10:52.614 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:52.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:52.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:52.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:52.614 INFO  Funcotator - Deflater: IntelDeflater
18:10:52.614 INFO  Funcotator - Inflater: IntelInflater
18:10:52.614 INFO  Funcotator - GCS max retries/reopens: 20
18:10:52.614 INFO  Funcotator - Requester pays: disabled
18:10:52.614 INFO  Funcotator - Initializing engine
18:10:52.615 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:10:52.616 INFO  Funcotator - Done initializing engine
18:10:52.616 INFO  Funcotator - Skipping sequence dictionary validation.
18:10:52.616 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:52.616 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9637959433836428093/TranscriptIdFile.txt
18:10:52.616 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
18:10:52.616 INFO  FuncotatorEngine - Transcript parsing complete.
18:10:52.616 INFO  Funcotator - Initializing data sources...
18:10:52.616 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:52.616 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:52.616 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:52.616 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:52.617 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:52.618 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:52.618 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:52.618 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:52.618 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:52.618 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:52.619 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:52.619 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:52.619 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:52.619 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:52.619 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:52.663 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:52.682 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:52.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:52.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:52.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:52.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:53.292 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:53.331 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:53.331 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:53.332 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:53.332 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:53.413 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:53.414 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:53.414 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:53.441 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:53.441 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:53.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:53.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:53.443 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:53.443 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:53.443 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:53.446 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:53.449 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:53.451 INFO  Funcotator - Initializing Funcotator Engine...
18:10:53.451 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:10:53.451 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:10:53.451 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.412146155635863701025.maf
18:10:53.451 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:10:53.452 INFO  ProgressMeter - Starting traversal
18:10:53.452 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:53.572 INFO  ProgressMeter -             unmapped              0.0                     4           2000.0
18:10:53.572 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:10:53.572 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:10:53.572 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2915041280
18:10:53.642 INFO  Funcotator - ------------------------------------------------------------
18:10:53.642 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:53.642 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:53.642 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:53.642 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:53.642 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:53 PM UTC
18:10:53.642 INFO  Funcotator - ------------------------------------------------------------
18:10:53.642 INFO  Funcotator - ------------------------------------------------------------
18:10:53.642 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:53.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:53.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:53.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:53.642 INFO  Funcotator - Deflater: IntelDeflater
18:10:53.642 INFO  Funcotator - Inflater: IntelInflater
18:10:53.642 INFO  Funcotator - GCS max retries/reopens: 20
18:10:53.642 INFO  Funcotator - Requester pays: disabled
18:10:53.642 INFO  Funcotator - Initializing engine
18:10:53.648 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
18:10:53.649 INFO  Funcotator - Done initializing engine
18:10:53.649 INFO  Funcotator - Validating sequence dictionaries...
18:10:53.650 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:53.650 INFO  Funcotator - Initializing data sources...
18:10:53.650 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:53.650 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:53.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:53.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:53.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:53.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:53.652 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:53.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:53.653 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:53.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:53.715 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:53.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:53.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:53.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:53.723 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:54.282 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:54.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:54.320 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:54.321 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:54.322 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:54.450 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:54.450 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:54.451 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:54.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:54.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:54.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:54.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:54.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:54.479 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:54.480 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:54.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:54.485 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:54.487 INFO  Funcotator - Initializing Funcotator Engine...
18:10:54.487 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:10:54.487 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:10:54.487 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11777799966604697801.vcf
18:10:54.489 INFO  ProgressMeter - Starting traversal
18:10:54.489 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:56.843 INFO  ProgressMeter -             unmapped              0.0                   198           5046.7
18:10:56.843 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:10:56.843 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:10:56.852 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2915041280
18:10:56.853 WARN  gatk -   VCF Elapsed Time: 3.278845027s
18:10:56.854 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator11777799966604697801.vcf
18:10:56.857 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
18:10:56.928 INFO  Funcotator - ------------------------------------------------------------
18:10:56.928 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:10:56.928 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:10:56.928 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:10:56.928 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:10:56.928 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:10:56 PM UTC
18:10:56.928 INFO  Funcotator - ------------------------------------------------------------
18:10:56.928 INFO  Funcotator - ------------------------------------------------------------
18:10:56.928 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:10:56.928 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:10:56.928 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:10:56.928 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:10:56.928 INFO  Funcotator - Deflater: IntelDeflater
18:10:56.928 INFO  Funcotator - Inflater: IntelInflater
18:10:56.928 INFO  Funcotator - GCS max retries/reopens: 20
18:10:56.928 INFO  Funcotator - Requester pays: disabled
18:10:56.928 INFO  Funcotator - Initializing engine
18:10:56.931 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
18:10:56.932 INFO  Funcotator - Done initializing engine
18:10:56.932 INFO  Funcotator - Validating sequence dictionaries...
18:10:56.932 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:10:56.932 INFO  Funcotator - Initializing data sources...
18:10:56.932 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:10:56.933 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:10:56.933 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:56.933 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:56.933 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:56.934 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:56.935 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:56.935 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:56.935 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:56.935 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:56.935 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:56.936 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:56.936 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:10:56.936 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:10:56.936 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:10:56.982 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:10:57.000 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:10:57.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:10:57.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:10:57.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:10:57.009 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:10:57.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:10:57.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:57.650 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:10:57.651 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:10:57.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:10:57.733 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:10:57.734 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:57.734 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:10:57.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:10:57.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:10:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:10:57.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:10:57.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:10:57.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:57.763 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:10:57.764 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:57.766 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:57.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:10:57.772 INFO  Funcotator - Initializing Funcotator Engine...
18:10:57.772 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:10:57.772 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:10:57.772 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator8099085403468342463.maf
18:10:57.772 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:10:57.774 INFO  ProgressMeter - Starting traversal
18:10:57.774 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:10:59.965 INFO  ProgressMeter -             unmapped              0.0                   198           5422.2
18:10:59.965 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:10:59.965 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:10:59.965 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:10:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2915041280
18:10:59.966 WARN  gatk -   MAF Elapsed Time: 3.104572669s
18:11:00.035 INFO  Funcotator - ------------------------------------------------------------
18:11:00.035 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:00.035 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:00.035 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:00.035 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:00.035 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:00 PM UTC
18:11:00.035 INFO  Funcotator - ------------------------------------------------------------
18:11:00.035 INFO  Funcotator - ------------------------------------------------------------
18:11:00.035 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:00.035 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:00.035 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:00.035 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:00.035 INFO  Funcotator - Deflater: IntelDeflater
18:11:00.035 INFO  Funcotator - Inflater: IntelInflater
18:11:00.035 INFO  Funcotator - GCS max retries/reopens: 20
18:11:00.035 INFO  Funcotator - Requester pays: disabled
18:11:00.035 INFO  Funcotator - Initializing engine
18:11:00.037 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
18:11:00.038 INFO  Funcotator - Done initializing engine
18:11:00.038 INFO  Funcotator - Validating sequence dictionaries...
18:11:00.038 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:00.039 INFO  Funcotator - Initializing data sources...
18:11:00.039 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:00.039 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:00.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:00.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:00.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:00.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:00.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:00.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:00.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:00.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:00.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:00.041 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:00.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:00.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:00.085 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:00.104 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:00.111 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:00.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:00.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:00.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:00.698 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:00.737 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:00.737 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:00.738 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:00.738 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:00.820 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:00.820 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:00.821 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:00.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:00.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:00.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:00.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:00.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:00.850 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:00.850 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:00.853 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:00.855 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:00.857 INFO  Funcotator - Initializing Funcotator Engine...
18:11:00.858 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:00.858 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:00.858 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator4042252057381263883.vcf
18:11:00.859 INFO  ProgressMeter - Starting traversal
18:11:00.859 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:01.953 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
18:11:01.953 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
18:11:02.824 INFO  ProgressMeter -             unmapped              0.0                   168           5129.8
18:11:02.824 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
18:11:02.824 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
18:11:02.830 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2915041280
18:11:02.830 WARN  gatk -   VCF Elapsed Time: 2.862048573s
18:11:02.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator4042252057381263883.vcf
18:11:02.833 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
18:11:02.907 INFO  Funcotator - ------------------------------------------------------------
18:11:02.907 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:02.907 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:02.907 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:02.907 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:02.907 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:02 PM UTC
18:11:02.907 INFO  Funcotator - ------------------------------------------------------------
18:11:02.907 INFO  Funcotator - ------------------------------------------------------------
18:11:02.907 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:02.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:02.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:02.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:02.907 INFO  Funcotator - Deflater: IntelDeflater
18:11:02.907 INFO  Funcotator - Inflater: IntelInflater
18:11:02.907 INFO  Funcotator - GCS max retries/reopens: 20
18:11:02.907 INFO  Funcotator - Requester pays: disabled
18:11:02.907 INFO  Funcotator - Initializing engine
18:11:02.909 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
18:11:02.910 INFO  Funcotator - Done initializing engine
18:11:02.910 INFO  Funcotator - Validating sequence dictionaries...
18:11:02.910 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:02.910 INFO  Funcotator - Initializing data sources...
18:11:02.910 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:02.910 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:02.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:02.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:02.913 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:02.913 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:02.913 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:02.913 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:02.913 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:02.913 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:02.956 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:02.975 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:02.983 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:02.983 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:02.983 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:02.984 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:03.575 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:03.648 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:03.648 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:03.649 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:03.649 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:03.732 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:03.732 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:03.733 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:03.760 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:03.760 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:03.760 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:03.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:03.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:03.761 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:03.762 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:03.765 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:03.768 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:03.770 INFO  Funcotator - Initializing Funcotator Engine...
18:11:03.770 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:03.770 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:03.770 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator8592670459416310234.maf
18:11:03.770 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:03.772 INFO  ProgressMeter - Starting traversal
18:11:03.772 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:04.839 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
18:11:04.839 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
18:11:05.688 INFO  ProgressMeter -             unmapped              0.0                   168           5261.0
18:11:05.688 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
18:11:05.688 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
18:11:05.688 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:05 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2946498560
18:11:05.689 WARN  gatk -   MAF Elapsed Time: 2.851923094s
18:11:05.757 INFO  Funcotator - ------------------------------------------------------------
18:11:05.757 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:05.757 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:05.757 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:05.757 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:05.757 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:05 PM UTC
18:11:05.757 INFO  Funcotator - ------------------------------------------------------------
18:11:05.757 INFO  Funcotator - ------------------------------------------------------------
18:11:05.757 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:05.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:05.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:05.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:05.757 INFO  Funcotator - Deflater: IntelDeflater
18:11:05.757 INFO  Funcotator - Inflater: IntelInflater
18:11:05.757 INFO  Funcotator - GCS max retries/reopens: 20
18:11:05.757 INFO  Funcotator - Requester pays: disabled
18:11:05.757 INFO  Funcotator - Initializing engine
18:11:05.759 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
18:11:05.760 INFO  Funcotator - Done initializing engine
18:11:05.760 INFO  Funcotator - Validating sequence dictionaries...
18:11:05.761 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:05.761 INFO  Funcotator - Initializing data sources...
18:11:05.761 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:05.761 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:05.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:05.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:05.761 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:05.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:05.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:05.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:05.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:05.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:05.763 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:05.763 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:05.764 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:05.764 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:05.807 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:05.827 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:05.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:05.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:05.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:05.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:06.444 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:06.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:06.482 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:06.483 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:06.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:06.565 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:06.565 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:06.566 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:06.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:06.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:06.594 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:06.594 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:06.595 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:06.595 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:06.595 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:06.597 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:06.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:06.602 INFO  Funcotator - Initializing Funcotator Engine...
18:11:06.602 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:06.602 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:06.602 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator16105913466132632454.vcf
18:11:06.604 INFO  ProgressMeter - Starting traversal
18:11:06.604 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:06.614 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
18:11:06.614 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:06.615 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:06.616 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:06 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2946498560
18:11:06.616 WARN  gatk -   VCF Elapsed Time: 0.925682722s
18:11:06.617 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator16105913466132632454.vcf
18:11:06.618 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
18:11:06.685 INFO  Funcotator - ------------------------------------------------------------
18:11:06.686 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:06.686 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:06.686 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:06.686 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:06.686 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:06 PM UTC
18:11:06.686 INFO  Funcotator - ------------------------------------------------------------
18:11:06.686 INFO  Funcotator - ------------------------------------------------------------
18:11:06.686 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:06.686 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:06.686 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:06.686 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:06.686 INFO  Funcotator - Deflater: IntelDeflater
18:11:06.686 INFO  Funcotator - Inflater: IntelInflater
18:11:06.686 INFO  Funcotator - GCS max retries/reopens: 20
18:11:06.686 INFO  Funcotator - Requester pays: disabled
18:11:06.686 INFO  Funcotator - Initializing engine
18:11:06.688 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
18:11:06.689 INFO  Funcotator - Done initializing engine
18:11:06.689 INFO  Funcotator - Validating sequence dictionaries...
18:11:06.689 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:06.689 INFO  Funcotator - Initializing data sources...
18:11:06.689 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:06.689 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:06.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:06.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:06.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:06.691 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:06.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:06.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:06.806 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:06.813 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:06.813 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:06.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:06.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:07.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:07.477 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:07.477 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:07.478 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:07.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:07.567 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:07.567 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:07.568 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:07.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:07.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:07.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:07.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:07.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:07.613 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:07.614 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:07.616 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:07.618 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:07.621 INFO  Funcotator - Initializing Funcotator Engine...
18:11:07.621 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:07.621 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:07.621 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator1722408462649150262.maf
18:11:07.621 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:07.622 INFO  ProgressMeter - Starting traversal
18:11:07.622 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:07.633 INFO  ProgressMeter -             unmapped              0.0                     1           5454.5
18:11:07.633 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:07.633 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:07.633 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2977955840
18:11:07.633 WARN  gatk -   MAF Elapsed Time: 1.014579366s
18:11:07.703 INFO  Funcotator - ------------------------------------------------------------
18:11:07.703 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:07.703 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:07.703 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:07.703 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:07.703 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:07 PM UTC
18:11:07.703 INFO  Funcotator - ------------------------------------------------------------
18:11:07.703 INFO  Funcotator - ------------------------------------------------------------
18:11:07.703 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:07.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:07.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:07.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:07.703 INFO  Funcotator - Deflater: IntelDeflater
18:11:07.703 INFO  Funcotator - Inflater: IntelInflater
18:11:07.703 INFO  Funcotator - GCS max retries/reopens: 20
18:11:07.703 INFO  Funcotator - Requester pays: disabled
18:11:07.703 INFO  Funcotator - Initializing engine
18:11:07.739 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
18:11:07.762 INFO  Funcotator - Done initializing engine
18:11:07.762 INFO  Funcotator - Validating sequence dictionaries...
18:11:07.769 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:07.769 INFO  Funcotator - Initializing data sources...
18:11:07.769 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:07.769 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:07.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:07.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:07.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:07.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:07.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:07.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:07.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:07.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:07.772 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:07.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:07.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:07.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:07.842 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:07.843 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:07.843 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:07.843 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:08.657 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:08.721 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:08.721 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:08.722 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:08.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:08.723 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:08.724 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:08.724 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:08.724 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:08.725 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:08.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:08.728 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:08.729 INFO  Funcotator - Initializing Funcotator Engine...
18:11:08.733 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:08.733 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator312864438453939976.vcf
18:11:08.751 INFO  ProgressMeter - Starting traversal
18:11:08.751 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:08.779 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000374877.7 for variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C): Reference allele runs off end of coding sequence.  Cannot yet handle this case.
18:11:08.782 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
18:11:08.786 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:08.791 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:08.791 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:08.791 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:08.791 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:08.791 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:08.792 INFO  ProgressMeter -             unmapped              0.0                     5           7317.1
18:11:08.792 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
18:11:08.792 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:08.809 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:08 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:08.810 WARN  gatk -   VCF Elapsed Time: 1.173599354s
18:11:08.810 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator312864438453939976.vcf
18:11:08.822 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
18:11:08.904 INFO  Funcotator - ------------------------------------------------------------
18:11:08.904 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:08.904 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:08.904 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:08.904 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:08.904 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:08 PM UTC
18:11:08.904 INFO  Funcotator - ------------------------------------------------------------
18:11:08.904 INFO  Funcotator - ------------------------------------------------------------
18:11:08.904 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:08.904 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:08.904 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:08.904 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:08.904 INFO  Funcotator - Deflater: IntelDeflater
18:11:08.904 INFO  Funcotator - Inflater: IntelInflater
18:11:08.904 INFO  Funcotator - GCS max retries/reopens: 20
18:11:08.904 INFO  Funcotator - Requester pays: disabled
18:11:08.904 INFO  Funcotator - Initializing engine
18:11:08.929 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
18:11:08.952 INFO  Funcotator - Done initializing engine
18:11:08.952 INFO  Funcotator - Validating sequence dictionaries...
18:11:08.964 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:08.964 INFO  Funcotator - Initializing data sources...
18:11:08.964 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:08.964 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:08.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:08.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:08.967 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:08.967 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:09.016 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:09.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:09.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:09.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:09.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:09.043 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:09.663 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:09.728 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:09.728 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:09.729 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:09.729 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:09.730 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:09.731 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:09.731 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:09.731 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:09.732 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:09.733 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:09.735 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:09.736 INFO  Funcotator - Initializing Funcotator Engine...
18:11:09.740 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:09.740 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator3340913665475431645.maf
18:11:09.741 INFO  ProgressMeter - Starting traversal
18:11:09.741 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:09.765 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000374877.7 for variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C): Reference allele runs off end of coding sequence.  Cannot yet handle this case.
18:11:09.766 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
18:11:09.768 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:09.771 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:09.771 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
18:11:09.771 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:09.771 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:09.771 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
18:11:09.772 INFO  ProgressMeter -             unmapped              0.0                     5           9677.4
18:11:09.772 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
18:11:09.773 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:09.773 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3116367872
18:11:09.773 WARN  gatk -   MAF Elapsed Time: 0.93925296s
18:11:09.842 INFO  Funcotator - ------------------------------------------------------------
18:11:09.843 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:09.843 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:09.843 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:09.843 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:09.843 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:09 PM UTC
18:11:09.843 INFO  Funcotator - ------------------------------------------------------------
18:11:09.843 INFO  Funcotator - ------------------------------------------------------------
18:11:09.843 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:09.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:09.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:09.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:09.843 INFO  Funcotator - Deflater: IntelDeflater
18:11:09.843 INFO  Funcotator - Inflater: IntelInflater
18:11:09.843 INFO  Funcotator - GCS max retries/reopens: 20
18:11:09.843 INFO  Funcotator - Requester pays: disabled
18:11:09.843 INFO  Funcotator - Initializing engine
18:11:09.845 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
18:11:09.847 INFO  Funcotator - Done initializing engine
18:11:09.847 INFO  Funcotator - Validating sequence dictionaries...
18:11:09.847 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:09.847 INFO  Funcotator - Initializing data sources...
18:11:09.847 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:09.847 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:09.847 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:09.847 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:09.847 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:09.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:09.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:09.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:09.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:09.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:09.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:09.850 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:09.850 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:09.850 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:09.850 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:09.893 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:09.911 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:09.918 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:09.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:09.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:09.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:10.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:10.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:10.593 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:10.594 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:10.594 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:10.675 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:10.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:10.676 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:10.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:10.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:10.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:10.705 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:10.705 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:10.705 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:10.706 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:10.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:10.711 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:10.713 INFO  Funcotator - Initializing Funcotator Engine...
18:11:10.713 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:10.713 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:10.713 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator17662062819600628987.vcf
18:11:10.717 INFO  ProgressMeter - Starting traversal
18:11:10.717 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:16.265 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
18:11:16.266 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
18:11:16.268 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16291.9
18:11:16.268 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
18:11:16.268 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
18:11:16.289 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:16 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3116367872
18:11:16.289 WARN  gatk -   VCF Elapsed Time: 6.514149326s
18:11:16.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator17662062819600628987.vcf
18:11:16.297 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
18:11:16.402 INFO  Funcotator - ------------------------------------------------------------
18:11:16.402 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:16.402 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:16.402 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:16.402 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:16.402 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:16 PM UTC
18:11:16.402 INFO  Funcotator - ------------------------------------------------------------
18:11:16.402 INFO  Funcotator - ------------------------------------------------------------
18:11:16.402 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:16.402 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:16.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:16.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:16.403 INFO  Funcotator - Deflater: IntelDeflater
18:11:16.403 INFO  Funcotator - Inflater: IntelInflater
18:11:16.403 INFO  Funcotator - GCS max retries/reopens: 20
18:11:16.403 INFO  Funcotator - Requester pays: disabled
18:11:16.403 INFO  Funcotator - Initializing engine
18:11:16.405 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
18:11:16.406 INFO  Funcotator - Done initializing engine
18:11:16.406 INFO  Funcotator - Validating sequence dictionaries...
18:11:16.406 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:16.406 INFO  Funcotator - Initializing data sources...
18:11:16.406 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:16.406 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:16.407 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:16.407 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:16.407 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:16.407 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:16.407 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:16.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:16.409 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:16.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:16.453 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:16.471 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:16.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:16.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:16.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:16.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:17.026 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:17.123 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:17.123 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:17.124 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:17.124 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:17.204 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:17.205 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:17.205 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:17.232 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:17.232 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:17	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:17.233 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:17.233 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:17.234 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:17.234 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:17.235 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:17.237 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:17.239 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:17.241 INFO  Funcotator - Initializing Funcotator Engine...
18:11:17.241 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:17.241 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:17.241 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator14150314382291016532.maf
18:11:17.242 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:17.242 INFO  ProgressMeter - Starting traversal
18:11:17.242 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:22.712 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
18:11:22.713 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
18:11:22.713 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16527.1
18:11:22.713 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
18:11:22.714 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
18:11:22.714 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:22 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3116367872
18:11:22.714 WARN  gatk -   MAF Elapsed Time: 6.380475507s
18:11:22.792 INFO  Funcotator - ------------------------------------------------------------
18:11:22.792 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:22.792 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:22.792 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:22.792 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:22.792 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:22 PM UTC
18:11:22.792 INFO  Funcotator - ------------------------------------------------------------
18:11:22.792 INFO  Funcotator - ------------------------------------------------------------
18:11:22.793 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:22.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:22.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:22.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:22.793 INFO  Funcotator - Deflater: IntelDeflater
18:11:22.793 INFO  Funcotator - Inflater: IntelInflater
18:11:22.793 INFO  Funcotator - GCS max retries/reopens: 20
18:11:22.793 INFO  Funcotator - Requester pays: disabled
18:11:22.793 INFO  Funcotator - Initializing engine
18:11:22.795 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
18:11:22.796 INFO  Funcotator - Done initializing engine
18:11:22.796 INFO  Funcotator - Validating sequence dictionaries...
18:11:22.796 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:22.796 INFO  Funcotator - Initializing data sources...
18:11:22.796 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:22.796 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:22.796 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:22.796 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:22.797 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:22.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:22.798 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:22.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:22.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:22.840 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:22.859 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:22.866 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:22.866 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:22.866 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:22.867 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:23.445 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:23.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:23.483 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:23.483 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:23.484 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:23.564 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:23.564 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:23.565 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:23.592 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:23.592 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:23	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:23.592 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:23.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:23.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:23.593 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:23.594 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:23.596 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:23.599 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:23.601 INFO  Funcotator - Initializing Funcotator Engine...
18:11:23.601 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:23.601 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:23.601 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator8051161328022739043.vcf
18:11:23.602 INFO  ProgressMeter - Starting traversal
18:11:23.602 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:25.705 INFO  ProgressMeter -             unmapped              0.0                   198           5649.1
18:11:25.705 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:11:25.705 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:11:25.714 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:25 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3116367872
18:11:25.782 INFO  Funcotator - ------------------------------------------------------------
18:11:25.782 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:25.782 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:25.782 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:25.782 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:25.782 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:25 PM UTC
18:11:25.782 INFO  Funcotator - ------------------------------------------------------------
18:11:25.782 INFO  Funcotator - ------------------------------------------------------------
18:11:25.782 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:25.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:25.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:25.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:25.782 INFO  Funcotator - Deflater: IntelDeflater
18:11:25.782 INFO  Funcotator - Inflater: IntelInflater
18:11:25.782 INFO  Funcotator - GCS max retries/reopens: 20
18:11:25.782 INFO  Funcotator - Requester pays: disabled
18:11:25.782 INFO  Funcotator - Initializing engine
18:11:25.785 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
18:11:25.786 INFO  Funcotator - Done initializing engine
18:11:25.786 INFO  Funcotator - Validating sequence dictionaries...
18:11:25.786 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:25.786 INFO  Funcotator - Initializing data sources...
18:11:25.786 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:25.786 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:25.786 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:25.786 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:25.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:25.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:25.789 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:25.789 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:25.789 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:25.876 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:25.895 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:25.902 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:25.903 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:25.903 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:25.904 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:26.453 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:26.494 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:26.494 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:26.494 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:26.495 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:26.577 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:26.577 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:26.578 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:26.605 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:26.605 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:26	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:26.605 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:26.606 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:26.606 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:26.606 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:26.607 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:26.609 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:26.612 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:26.614 INFO  Funcotator - Initializing Funcotator Engine...
18:11:26.614 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:26.614 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:26.614 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator11123830592053775343.maf
18:11:26.614 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:26.615 INFO  ProgressMeter - Starting traversal
18:11:26.615 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:28.774 INFO  ProgressMeter -             unmapped              0.0                   198           5502.5
18:11:28.774 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:11:28.774 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:11:28.775 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3116367872
18:11:28.846 INFO  Funcotator - ------------------------------------------------------------
18:11:28.846 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:28.846 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:28.846 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:28.846 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:28.846 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:28 PM UTC
18:11:28.846 INFO  Funcotator - ------------------------------------------------------------
18:11:28.846 INFO  Funcotator - ------------------------------------------------------------
18:11:28.846 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:28.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:28.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:28.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:28.846 INFO  Funcotator - Deflater: IntelDeflater
18:11:28.846 INFO  Funcotator - Inflater: IntelInflater
18:11:28.846 INFO  Funcotator - GCS max retries/reopens: 20
18:11:28.846 INFO  Funcotator - Requester pays: disabled
18:11:28.846 INFO  Funcotator - Initializing engine
18:11:28.849 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
18:11:28.851 INFO  Funcotator - Done initializing engine
18:11:28.851 INFO  Funcotator - Validating sequence dictionaries...
18:11:28.851 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:28.851 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:28.920 INFO  Funcotator - ------------------------------------------------------------
18:11:28.920 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:28.920 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:28.920 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:28.920 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:28.920 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:28 PM UTC
18:11:28.920 INFO  Funcotator - ------------------------------------------------------------
18:11:28.920 INFO  Funcotator - ------------------------------------------------------------
18:11:28.920 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:28.920 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:28.920 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:28.920 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:28.920 INFO  Funcotator - Deflater: IntelDeflater
18:11:28.920 INFO  Funcotator - Inflater: IntelInflater
18:11:28.920 INFO  Funcotator - GCS max retries/reopens: 20
18:11:28.920 INFO  Funcotator - Requester pays: disabled
18:11:28.920 INFO  Funcotator - Initializing engine
18:11:28.922 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:11:28.941 INFO  Funcotator - Done initializing engine
18:11:28.941 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:28.941 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:28.941 INFO  Funcotator - Initializing data sources...
18:11:28.941 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:28.942 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:28.942 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:28.942 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:28.942 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:28.942 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:28.942 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:28.942 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:28.943 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:28.943 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:28.944 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:28.944 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:28.944 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:28.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:28.963 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:28.971 INFO  Funcotator - Initializing Funcotator Engine...
18:11:28.979 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:28.979 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16387098136851248671.vcf
18:11:28.992 INFO  ProgressMeter - Starting traversal
18:11:28.992 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:29.026 INFO  ProgressMeter -             unmapped              0.0                   100         176470.6
18:11:29.026 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
18:11:29.026 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:29.031 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:29.032 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16387098136851248671.vcf
18:11:29.113 INFO  Funcotator - ------------------------------------------------------------
18:11:29.113 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:29.113 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:29.113 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:29.113 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:29.113 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:29 PM UTC
18:11:29.113 INFO  Funcotator - ------------------------------------------------------------
18:11:29.113 INFO  Funcotator - ------------------------------------------------------------
18:11:29.113 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:29.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:29.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:29.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:29.113 INFO  Funcotator - Deflater: IntelDeflater
18:11:29.113 INFO  Funcotator - Inflater: IntelInflater
18:11:29.113 INFO  Funcotator - GCS max retries/reopens: 20
18:11:29.113 INFO  Funcotator - Requester pays: disabled
18:11:29.113 INFO  Funcotator - Initializing engine
18:11:29.114 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:11:29.117 INFO  Funcotator - Done initializing engine
18:11:29.117 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:29.117 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:29.117 INFO  Funcotator - Initializing data sources...
18:11:29.117 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:29.117 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:29.117 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:29.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:29.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:29.118 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:29.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:29.118 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:29.119 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:29.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:29.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:29.119 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:29.120 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:29.121 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:29.123 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:29.124 INFO  Funcotator - Initializing Funcotator Engine...
18:11:29.124 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:29.124 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:29.124 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11138564614499724166.vcf
18:11:29.130 INFO  ProgressMeter - Starting traversal
18:11:29.130 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:29.138 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
18:11:29.138 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:11:29.138 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:11:29.141 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:29.142 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11138564614499724166.vcf
18:11:29.212 INFO  Funcotator - ------------------------------------------------------------
18:11:29.213 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:29.213 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:29.213 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:29.213 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:29.213 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:29 PM UTC
18:11:29.213 INFO  Funcotator - ------------------------------------------------------------
18:11:29.213 INFO  Funcotator - ------------------------------------------------------------
18:11:29.213 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:29.213 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:29.213 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:29.213 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:29.213 INFO  Funcotator - Deflater: IntelDeflater
18:11:29.213 INFO  Funcotator - Inflater: IntelInflater
18:11:29.213 INFO  Funcotator - GCS max retries/reopens: 20
18:11:29.213 INFO  Funcotator - Requester pays: disabled
18:11:29.213 INFO  Funcotator - Initializing engine
18:11:29.214 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
18:11:29.239 INFO  Funcotator - Done initializing engine
18:11:29.239 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:29.239 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:29.239 INFO  Funcotator - Initializing data sources...
18:11:29.240 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:29.240 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:29.240 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:29.240 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:29.240 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:29.240 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:29.240 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:29.240 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:29.241 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:29.241 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:29.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:29.242 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:29.242 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:29.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:29.275 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:29.284 INFO  Funcotator - Initializing Funcotator Engine...
18:11:29.288 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:29.288 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7140851741205426855.vcf
18:11:29.299 INFO  ProgressMeter - Starting traversal
18:11:29.299 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:29.304 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
18:11:29.304 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
18:11:29.304 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.304 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:29.304 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
18:11:29.304 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
18:11:29.307 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.307 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:29.307 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
18:11:29.307 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
18:11:29.307 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
18:11:29.308 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
18:11:29.308 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.308 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:29.308 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
18:11:29.308 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
18:11:29.308 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
18:11:29.308 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
18:11:29.308 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
18:11:29.309 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
18:11:29.309 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
18:11:29.309 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
18:11:29.309 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.309 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:29.310 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
18:11:29.310 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
18:11:29.310 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.310 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:29.310 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
18:11:29.311 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
18:11:29.311 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
18:11:29.311 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
18:11:29.311 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
18:11:29.311 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:29.311 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
18:11:29.311 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
18:11:29.312 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
18:11:29.312 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
18:11:29.312 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.312 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:29.312 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
18:11:29.312 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
18:11:29.313 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
18:11:29.313 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:29.313 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
18:11:29.313 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
18:11:29.314 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
18:11:29.314 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
18:11:29.314 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:29.315 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:29.315 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
18:11:29.315 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
18:11:29.315 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
18:11:29.315 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
18:11:29.316 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:29.323 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:29.324 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7140851741205426855.vcf
18:11:29.405 INFO  Funcotator - ------------------------------------------------------------
18:11:29.405 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:29.405 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:29.405 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:29.405 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:29.405 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:29 PM UTC
18:11:29.405 INFO  Funcotator - ------------------------------------------------------------
18:11:29.405 INFO  Funcotator - ------------------------------------------------------------
18:11:29.405 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:29.405 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:29.405 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:29.405 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:29.405 INFO  Funcotator - Deflater: IntelDeflater
18:11:29.405 INFO  Funcotator - Inflater: IntelInflater
18:11:29.405 INFO  Funcotator - GCS max retries/reopens: 20
18:11:29.405 INFO  Funcotator - Requester pays: disabled
18:11:29.405 INFO  Funcotator - Initializing engine
18:11:29.408 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
18:11:29.409 INFO  Funcotator - Done initializing engine
18:11:29.409 INFO  Funcotator - Validating sequence dictionaries...
18:11:29.409 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:29.410 INFO  Funcotator - Initializing data sources...
18:11:29.410 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:29.410 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:29.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:29.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:29.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:29.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:29.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:29.412 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:29.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:29.413 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:29.456 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:29.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:29.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:29.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:29.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:29.484 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:30.092 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:30.129 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:30.129 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:30.130 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:30.131 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:30.212 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:30.213 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:30.213 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:30.241 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:30.241 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:30	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:30.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:30.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:30.243 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:30.243 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:30.243 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:30.246 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:30.248 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:30.250 INFO  Funcotator - Initializing Funcotator Engine...
18:11:30.250 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:30.250 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:30.251 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator12275748570169516462.vcf
18:11:30.254 INFO  ProgressMeter - Starting traversal
18:11:30.254 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:30.307 INFO  ProgressMeter -             unmapped              0.0                     1           1132.1
18:11:30.307 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:30.307 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:30.307 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:30 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:30.308 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator12275748570169516462.vcf
18:11:30.375 INFO  Funcotator - ------------------------------------------------------------
18:11:30.375 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:30.375 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:30.375 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:30.375 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:30.375 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:30 PM UTC
18:11:30.375 INFO  Funcotator - ------------------------------------------------------------
18:11:30.375 INFO  Funcotator - ------------------------------------------------------------
18:11:30.375 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:30.375 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:30.375 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:30.375 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:30.375 INFO  Funcotator - Deflater: IntelDeflater
18:11:30.375 INFO  Funcotator - Inflater: IntelInflater
18:11:30.375 INFO  Funcotator - GCS max retries/reopens: 20
18:11:30.375 INFO  Funcotator - Requester pays: disabled
18:11:30.375 INFO  Funcotator - Initializing engine
18:11:30.377 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
18:11:30.379 INFO  Funcotator - Done initializing engine
18:11:30.379 INFO  Funcotator - Validating sequence dictionaries...
18:11:30.379 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:30.379 INFO  Funcotator - Initializing data sources...
18:11:30.379 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:30.379 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:30.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:30.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:30.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:30.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:30.381 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:30.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:30.382 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:30.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:30.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:30.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:30.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:30.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:30.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:31.033 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:31.072 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:31.072 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:31.073 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:31.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:31.202 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:31.202 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:31.203 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:31.231 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:31.231 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:31.231 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:31.232 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:31.232 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:31.232 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:31.233 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:31.235 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:31.238 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:31.240 INFO  Funcotator - Initializing Funcotator Engine...
18:11:31.240 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:31.240 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:31.240 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator5061945340911917451.vcf
18:11:31.244 INFO  ProgressMeter - Starting traversal
18:11:31.244 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:31.251 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.305 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
18:11:31.311 INFO  ProgressMeter -             unmapped              0.0                     2           1791.0
18:11:31.311 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:11:31.311 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:31.311 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:31 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:31.312 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator5061945340911917451.vcf
18:11:31.383 INFO  Funcotator - ------------------------------------------------------------
18:11:31.383 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:31.383 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:31.383 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:31.383 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:31.383 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:31 PM UTC
18:11:31.383 INFO  Funcotator - ------------------------------------------------------------
18:11:31.383 INFO  Funcotator - ------------------------------------------------------------
18:11:31.383 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:31.383 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:31.383 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:31.383 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:31.383 INFO  Funcotator - Deflater: IntelDeflater
18:11:31.383 INFO  Funcotator - Inflater: IntelInflater
18:11:31.383 INFO  Funcotator - GCS max retries/reopens: 20
18:11:31.383 INFO  Funcotator - Requester pays: disabled
18:11:31.383 INFO  Funcotator - Initializing engine
18:11:31.385 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
18:11:31.386 INFO  Funcotator - Done initializing engine
18:11:31.386 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:31.386 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:31.386 INFO  Funcotator - Initializing data sources...
18:11:31.386 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:31.386 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:31.386 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:31.386 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:31.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:31.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:31.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:31.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:31.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:31.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:31.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:31.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:31.389 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:31.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:31.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:31.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:31.452 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:31.459 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:31.460 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:31.460 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:31.460 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:32.076 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:32.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:32.114 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:32.115 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:32.115 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:32.196 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:32.196 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:32.197 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:32.224 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:32.224 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:32	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:32.225 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:32.225 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:32.226 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:32.226 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:32.226 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:32.228 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:32.231 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:32.233 INFO  Funcotator - Initializing Funcotator Engine...
18:11:32.233 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:32.233 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:32.234 INFO  FuncotatorUtils - Setting custom variant classification severities from: file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_order_for_int_test.tsv
18:11:32.234 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
18:11:32.234 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
18:11:32.234 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9786244737393933725.vcf
18:11:32.238 INFO  ProgressMeter - Starting traversal
18:11:32.238 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:32.274 INFO  ProgressMeter -             unmapped              0.0                     1           1666.7
18:11:32.274 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:32.274 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:32.274 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:32 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3116367872
18:11:32.275 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9786244737393933725.vcf
18:11:32.276 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_expected_out.vcf
[May 27, 2025 at 6:11:32 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
[May 27, 2025 at 6:11:32 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:32.520 INFO  Funcotator - ------------------------------------------------------------
18:11:32.520 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:32.520 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:32.520 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:32.520 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:32.520 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:32 PM UTC
18:11:32.520 INFO  Funcotator - ------------------------------------------------------------
18:11:32.520 INFO  Funcotator - ------------------------------------------------------------
18:11:32.520 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:32.520 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:32.520 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:32.520 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:32.520 INFO  Funcotator - Deflater: IntelDeflater
18:11:32.520 INFO  Funcotator - Inflater: IntelInflater
18:11:32.520 INFO  Funcotator - GCS max retries/reopens: 20
18:11:32.520 INFO  Funcotator - Requester pays: disabled
18:11:32.520 INFO  Funcotator - Initializing engine
18:11:32.521 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:11:32.538 INFO  Funcotator - Done initializing engine
18:11:32.538 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:32.538 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:32.538 INFO  Funcotator - Initializing data sources...
18:11:32.538 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:32.538 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:32.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:32.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:32.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:32.538 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:32.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:32.539 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:32.539 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:32.539 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:32.540 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:32.540 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:32.540 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:32.548 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:32.557 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:32.565 INFO  Funcotator - Initializing Funcotator Engine...
18:11:32.571 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:32.571 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16611715715476987763.vcf
18:11:32.584 INFO  ProgressMeter - Starting traversal
18:11:32.584 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:32.609 INFO  ProgressMeter -             unmapped              0.0                   100         240000.0
18:11:32.609 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
18:11:32.609 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:32.614 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:32 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:32.615 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16611715715476987763.vcf
18:11:32.697 INFO  Funcotator - ------------------------------------------------------------
18:11:32.697 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:32.697 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:32.697 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:32.697 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:32.697 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:32 PM UTC
18:11:32.697 INFO  Funcotator - ------------------------------------------------------------
18:11:32.697 INFO  Funcotator - ------------------------------------------------------------
18:11:32.697 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:32.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:32.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:32.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:32.697 INFO  Funcotator - Deflater: IntelDeflater
18:11:32.697 INFO  Funcotator - Inflater: IntelInflater
18:11:32.697 INFO  Funcotator - GCS max retries/reopens: 20
18:11:32.697 INFO  Funcotator - Requester pays: disabled
18:11:32.697 INFO  Funcotator - Initializing engine
18:11:32.700 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
18:11:32.700 INFO  Funcotator - Done initializing engine
18:11:32.700 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:32.700 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:32.700 INFO  Funcotator - Initializing data sources...
18:11:32.700 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/
18:11:32.701 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:32.701 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:32.701 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:32.701 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
18:11:32.701 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:32.701 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:32.701 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:32.702 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:32.702 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:32.702 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
18:11:32.702 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
18:11:32.703 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
18:11:32.705 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
18:11:32.708 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
18:11:32.710 INFO  Funcotator - Initializing Funcotator Engine...
18:11:32.710 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:32.710 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:32.710 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:32.710 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing5954561542015790297.vcf
18:11:32.713 INFO  ProgressMeter - Starting traversal
18:11:32.713 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:32.737 INFO  ProgressMeter -             unmapped              0.0                     1           2500.0
18:11:32.737 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:32.737 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
18:11:32.740 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:32 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3116367872
18:11:32.740 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing5954561542015790297.vcf
18:11:32.810 INFO  Funcotator - ------------------------------------------------------------
18:11:32.810 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:32.810 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:32.810 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:32.810 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:32.810 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:32 PM UTC
18:11:32.810 INFO  Funcotator - ------------------------------------------------------------
18:11:32.810 INFO  Funcotator - ------------------------------------------------------------
18:11:32.811 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:32.811 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:32.811 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:32.811 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:32.811 INFO  Funcotator - Deflater: IntelDeflater
18:11:32.811 INFO  Funcotator - Inflater: IntelInflater
18:11:32.811 INFO  Funcotator - GCS max retries/reopens: 20
18:11:32.811 INFO  Funcotator - Requester pays: disabled
18:11:32.811 INFO  Funcotator - Initializing engine
18:11:32.812 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:11:32.813 INFO  Funcotator - Done initializing engine
18:11:32.813 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:32.813 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:32.813 INFO  Funcotator - Initializing data sources...
18:11:32.813 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:32.813 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:32.813 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:32.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:32.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:32.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:32.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:32.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:32.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:32.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:32.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:32.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:32.816 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:32.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:32.817 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:32.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:32.946 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:32.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:32.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:32.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:32.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:33.543 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:33.580 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:33.580 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:33.581 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:33.582 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:33.662 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:33.663 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:33.663 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:33.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:33.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:33	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:33.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:33.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:33.693 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:33.693 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:33.694 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:33.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:33.698 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:33.700 INFO  Funcotator - Initializing Funcotator Engine...
18:11:33.700 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:33.701 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:11:33.701 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:11:33.701 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:11:33.701 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:11:33.701 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:33.701 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7847252509668092694.vcf
18:11:33.701 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:33.702 INFO  ProgressMeter - Starting traversal
18:11:33.702 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:33.724 INFO  ProgressMeter -             unmapped              0.0                     3           8181.8
18:11:33.724 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:11:33.724 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:33.727 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:33 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:33.791 INFO  Funcotator - ------------------------------------------------------------
18:11:33.791 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:33.791 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:33.791 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:33.791 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:33.791 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:33 PM UTC
18:11:33.791 INFO  Funcotator - ------------------------------------------------------------
18:11:33.791 INFO  Funcotator - ------------------------------------------------------------
18:11:33.791 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:33.791 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:33.791 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:33.791 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:33.791 INFO  Funcotator - Deflater: IntelDeflater
18:11:33.791 INFO  Funcotator - Inflater: IntelInflater
18:11:33.791 INFO  Funcotator - GCS max retries/reopens: 20
18:11:33.791 INFO  Funcotator - Requester pays: disabled
18:11:33.791 INFO  Funcotator - Initializing engine
18:11:33.792 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:11:33.792 INFO  Funcotator - Done initializing engine
18:11:33.792 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:33.792 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:33.792 INFO  Funcotator - Initializing data sources...
18:11:33.792 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:33.792 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:33.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:33.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:33.795 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:33.795 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:33.795 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:33.795 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:33.795 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:33.837 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:33.856 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:33.863 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:33.863 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:33.864 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:33.864 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:34.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:34.480 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:34.480 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:34.480 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:34.481 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:34.602 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:34.603 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:34.603 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:34.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:34.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:34	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:34.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:34.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:34.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:34.632 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:34.633 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:34.635 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:34.639 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:34.641 INFO  Funcotator - Initializing Funcotator Engine...
18:11:34.641 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:34.641 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:34.641 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15107149655710627948.vcf
18:11:34.642 INFO  ProgressMeter - Starting traversal
18:11:34.642 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:34.754 INFO  ProgressMeter -             unmapped              0.0                     4           2142.9
18:11:34.754 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:11:34.754 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:34.754 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:34 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:34.818 INFO  Funcotator - ------------------------------------------------------------
18:11:34.818 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:34.819 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:34.819 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:34.819 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:34.819 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:34 PM UTC
18:11:34.819 INFO  Funcotator - ------------------------------------------------------------
18:11:34.819 INFO  Funcotator - ------------------------------------------------------------
18:11:34.819 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:34.819 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:34.819 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:34.819 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:34.819 INFO  Funcotator - Deflater: IntelDeflater
18:11:34.819 INFO  Funcotator - Inflater: IntelInflater
18:11:34.819 INFO  Funcotator - GCS max retries/reopens: 20
18:11:34.819 INFO  Funcotator - Requester pays: disabled
18:11:34.819 INFO  Funcotator - Initializing engine
18:11:34.820 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:11:34.821 INFO  Funcotator - Done initializing engine
18:11:34.821 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:34.821 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:34.821 INFO  Funcotator - Initializing data sources...
18:11:34.821 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:34.821 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:34.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:34.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:34.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:34.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:34.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:34.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:34.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:34.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:34.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:34.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:34.824 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:34.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:34.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:34.872 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:34.891 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:34.898 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:34.898 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:34.899 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:34.899 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:35.576 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:35.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:35.614 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:35.615 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:35.616 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:35.697 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:35.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:35.698 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:35.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:35.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:35.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:35.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:35.727 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:35.727 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:35.728 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:35.730 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:35.732 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:35.734 INFO  Funcotator - Initializing Funcotator Engine...
18:11:35.734 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:35.735 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:11:35.735 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:11:35.735 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:11:35.735 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:11:35.735 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:35.735 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2575358727291889623.vcf
18:11:35.736 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:35.737 INFO  ProgressMeter - Starting traversal
18:11:35.737 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:35.761 INFO  ProgressMeter -             unmapped              0.0                     3           7500.0
18:11:35.762 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:11:35.762 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:35.764 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:35 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3116367872
18:11:35.831 INFO  Funcotator - ------------------------------------------------------------
18:11:35.831 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:35.831 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:35.831 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:35.831 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:35.831 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:35 PM UTC
18:11:35.831 INFO  Funcotator - ------------------------------------------------------------
18:11:35.831 INFO  Funcotator - ------------------------------------------------------------
18:11:35.831 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:35.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:35.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:35.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:35.831 INFO  Funcotator - Deflater: IntelDeflater
18:11:35.831 INFO  Funcotator - Inflater: IntelInflater
18:11:35.831 INFO  Funcotator - GCS max retries/reopens: 20
18:11:35.831 INFO  Funcotator - Requester pays: disabled
18:11:35.831 INFO  Funcotator - Initializing engine
18:11:35.832 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:11:35.833 INFO  Funcotator - Done initializing engine
18:11:35.833 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:35.833 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:35.833 INFO  Funcotator - Initializing data sources...
18:11:35.833 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:35.833 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:35.833 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:35.833 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:35.833 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:35.833 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:35.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:35.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:35.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:35.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:35.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:35.835 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:35.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:35.836 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:35.877 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:35.896 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:35.903 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:35.903 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:35.904 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:35.904 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:36.611 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:36.666 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:36.666 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:36.667 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:36.667 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:36.750 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:36.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:36.751 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:36.779 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:36.779 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:36.779 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:36.779 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:36.780 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:36.780 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:36.781 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:36.783 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:36.786 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:36.788 INFO  Funcotator - Initializing Funcotator Engine...
18:11:36.788 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:36.788 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:36.788 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5015908486637166463.vcf
18:11:36.789 INFO  ProgressMeter - Starting traversal
18:11:36.789 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:36.901 INFO  ProgressMeter -             unmapped              0.0                     4           2142.9
18:11:36.901 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:11:36.901 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:36.901 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:36 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3164602368
18:11:36.968 INFO  Funcotator - ------------------------------------------------------------
18:11:36.968 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:36.968 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:36.968 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:36.968 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:36.968 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:36 PM UTC
18:11:36.968 INFO  Funcotator - ------------------------------------------------------------
18:11:36.968 INFO  Funcotator - ------------------------------------------------------------
18:11:36.968 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:36.968 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:36.968 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:36.968 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:36.968 INFO  Funcotator - Deflater: IntelDeflater
18:11:36.968 INFO  Funcotator - Inflater: IntelInflater
18:11:36.968 INFO  Funcotator - GCS max retries/reopens: 20
18:11:36.968 INFO  Funcotator - Requester pays: disabled
18:11:36.968 INFO  Funcotator - Initializing engine
18:11:36.969 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:11:36.969 INFO  Funcotator - Done initializing engine
18:11:36.969 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:36.969 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:36.969 INFO  Funcotator - Initializing data sources...
18:11:36.969 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:36.969 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:36.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:36.971 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:36.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:36.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:36.972 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:36.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:36.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:37.015 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:37.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:37.102 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:37.102 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:37.102 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:37.103 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:37.736 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:37.774 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:37.774 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:37.775 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:37.775 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:37.857 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:37.857 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:37.858 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:37.885 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:37.885 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:37	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:37.886 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:37.886 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:37.886 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:37.886 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:37.887 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:37.889 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:37.892 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:37.894 INFO  Funcotator - Initializing Funcotator Engine...
18:11:37.894 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:37.894 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:11:37.894 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:11:37.894 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:11:37.894 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:11:37.894 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:11:37.894 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:11:37.894 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:11:37.895 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:11:37.895 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:37.895 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16507585181612917210.maf
18:11:37.896 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:37.896 INFO  ProgressMeter - Starting traversal
18:11:37.896 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:37.917 INFO  ProgressMeter -             unmapped              0.0                     3           8571.4
18:11:37.917 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:11:37.917 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:37.917 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3240099840
18:11:37.986 INFO  Funcotator - ------------------------------------------------------------
18:11:37.986 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:37.986 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:37.986 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:37.986 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:37.986 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:37 PM UTC
18:11:37.986 INFO  Funcotator - ------------------------------------------------------------
18:11:37.986 INFO  Funcotator - ------------------------------------------------------------
18:11:37.986 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:37.986 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:37.986 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:37.986 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:37.986 INFO  Funcotator - Deflater: IntelDeflater
18:11:37.986 INFO  Funcotator - Inflater: IntelInflater
18:11:37.986 INFO  Funcotator - GCS max retries/reopens: 20
18:11:37.986 INFO  Funcotator - Requester pays: disabled
18:11:37.986 INFO  Funcotator - Initializing engine
18:11:37.987 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:11:37.988 INFO  Funcotator - Done initializing engine
18:11:37.988 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:37.988 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:37.988 INFO  Funcotator - Initializing data sources...
18:11:37.988 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:37.988 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:37.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:37.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:37.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:37.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:37.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:37.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:37.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:37.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:37.990 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:37.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:37.991 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:38.069 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:38.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:38.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:38.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:38.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:38.096 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:38.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:38.809 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:38.809 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:38.809 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:38.810 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:38.894 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:38.895 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:38.895 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:38.922 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:38.922 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:38.923 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:38.923 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:38.924 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:38.924 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:38.924 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:38.926 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:38.929 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:38.931 INFO  Funcotator - Initializing Funcotator Engine...
18:11:38.931 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:38.931 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:38.931 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7869441600786092285.maf
18:11:38.932 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:38.932 INFO  ProgressMeter - Starting traversal
18:11:38.932 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:39.047 INFO  ProgressMeter -             unmapped              0.0                     4           2087.0
18:11:39.047 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:11:39.047 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:39.047 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:39 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2663383040
18:11:39.116 INFO  Funcotator - ------------------------------------------------------------
18:11:39.116 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:39.116 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:39.116 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:39.116 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:39.116 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:39 PM UTC
18:11:39.116 INFO  Funcotator - ------------------------------------------------------------
18:11:39.116 INFO  Funcotator - ------------------------------------------------------------
18:11:39.116 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:39.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:39.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:39.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:39.116 INFO  Funcotator - Deflater: IntelDeflater
18:11:39.116 INFO  Funcotator - Inflater: IntelInflater
18:11:39.116 INFO  Funcotator - GCS max retries/reopens: 20
18:11:39.116 INFO  Funcotator - Requester pays: disabled
18:11:39.116 INFO  Funcotator - Initializing engine
18:11:39.117 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
18:11:39.118 INFO  Funcotator - Done initializing engine
18:11:39.118 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:39.118 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:39.118 INFO  Funcotator - Initializing data sources...
18:11:39.118 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:39.118 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:39.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:39.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:39.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:39.120 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:39.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:39.121 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:39.165 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:39.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:39.191 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:39.191 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:39.191 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:39.192 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:39.867 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:39.906 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:39.906 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:39.907 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:39.907 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:39.989 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:39.989 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:39.990 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:40.017 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:40.017 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:40	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:40.017 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:40.018 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:40.018 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.018 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:40.019 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.021 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.024 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.026 INFO  Funcotator - Initializing Funcotator Engine...
18:11:40.026 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:11:40.026 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
18:11:40.026 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
18:11:40.026 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
18:11:40.026 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
18:11:40.027 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
18:11:40.027 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:40.027 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11564359269257558302.maf
18:11:40.027 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:40.027 INFO  ProgressMeter - Starting traversal
18:11:40.027 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:40.048 INFO  ProgressMeter -             unmapped              0.0                     3           8571.4
18:11:40.048 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
18:11:40.048 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:40.048 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2663383040
18:11:40.112 INFO  Funcotator - ------------------------------------------------------------
18:11:40.112 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:40.112 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:40.112 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:40.112 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:40.112 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:40 PM UTC
18:11:40.112 INFO  Funcotator - ------------------------------------------------------------
18:11:40.112 INFO  Funcotator - ------------------------------------------------------------
18:11:40.112 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:40.112 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:40.112 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:40.112 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:40.112 INFO  Funcotator - Deflater: IntelDeflater
18:11:40.112 INFO  Funcotator - Inflater: IntelInflater
18:11:40.112 INFO  Funcotator - GCS max retries/reopens: 20
18:11:40.112 INFO  Funcotator - Requester pays: disabled
18:11:40.112 INFO  Funcotator - Initializing engine
18:11:40.113 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
18:11:40.113 INFO  Funcotator - Done initializing engine
18:11:40.113 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:40.113 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:40.113 INFO  Funcotator - Initializing data sources...
18:11:40.113 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:40.113 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:40.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:40.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:40.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:40.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:40.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:40.126 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:40.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:40.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:40.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.128 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:40.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:40.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:40.171 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:40.190 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:40.197 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:40.198 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:40.198 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:40.198 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:40.802 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:40.840 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:40.840 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:40.841 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:40.841 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:40.922 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:40.923 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:40.923 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:40.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:40.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:40	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:40.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:40.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:40.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.951 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:40.952 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.957 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:40.959 INFO  Funcotator - Initializing Funcotator Engine...
18:11:40.959 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:40.959 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:40.959 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15215318257305359446.maf
18:11:40.959 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:40.959 INFO  ProgressMeter - Starting traversal
18:11:40.959 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.129 INFO  ProgressMeter -             unmapped              0.0                     4           1411.8
18:11:41.129 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:11:41.129 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
18:11:41.129 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2663383040
18:11:41.193 INFO  Funcotator - ------------------------------------------------------------
18:11:41.193 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.193 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.193 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.193 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.193 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.193 INFO  Funcotator - ------------------------------------------------------------
18:11:41.193 INFO  Funcotator - ------------------------------------------------------------
18:11:41.193 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.193 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.193 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.193 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.193 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.193 INFO  Funcotator - Inflater: IntelInflater
18:11:41.193 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.193 INFO  Funcotator - Requester pays: disabled
18:11:41.193 INFO  Funcotator - Initializing engine
18:11:41.194 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:11:41.217 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
18:11:41.217 INFO  Funcotator - Done initializing engine
18:11:41.217 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.217 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.217 INFO  Funcotator - Initializing data sources...
18:11:41.217 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
18:11:41.217 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.218 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.218 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
18:11:41.218 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.218 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.218 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.218 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.219 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.219 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
18:11:41.220 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.220 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.221 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.234 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.245 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.253 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.257 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:41.257 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6372005350136275047.vcf
18:11:41.269 INFO  ProgressMeter - Starting traversal
18:11:41.269 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.281 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
18:11:41.281 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
18:11:41.281 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:41.286 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.350 INFO  Funcotator - ------------------------------------------------------------
18:11:41.350 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.350 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.350 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.350 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.350 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.350 INFO  Funcotator - ------------------------------------------------------------
18:11:41.350 INFO  Funcotator - ------------------------------------------------------------
18:11:41.350 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.350 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.350 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.350 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.350 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.350 INFO  Funcotator - Inflater: IntelInflater
18:11:41.350 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.350 INFO  Funcotator - Requester pays: disabled
18:11:41.350 INFO  Funcotator - Initializing engine
18:11:41.351 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:11:41.372 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
18:11:41.372 INFO  Funcotator - Done initializing engine
18:11:41.372 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.372 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.372 INFO  Funcotator - Initializing data sources...
18:11:41.372 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
18:11:41.372 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.372 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.372 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
18:11:41.372 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.372 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.372 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.372 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.373 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
18:11:41.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v43.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
18:11:41.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.374 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.374 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.382 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.390 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.398 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.402 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:41.402 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15645855810554355617.vcf
18:11:41.414 INFO  ProgressMeter - Starting traversal
18:11:41.414 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.425 INFO  ProgressMeter -             unmapped              0.0                    32         174545.5
18:11:41.425 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
18:11:41.425 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:41.430 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.431 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6372005350136275047.vcf
18:11:41.440 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15645855810554355617.vcf
18:11:41.514 INFO  Funcotator - ------------------------------------------------------------
18:11:41.514 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.514 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.514 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.514 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.514 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.514 INFO  Funcotator - ------------------------------------------------------------
18:11:41.514 INFO  Funcotator - ------------------------------------------------------------
18:11:41.514 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.514 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.514 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.514 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.514 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.514 INFO  Funcotator - Inflater: IntelInflater
18:11:41.514 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.514 INFO  Funcotator - Requester pays: disabled
18:11:41.514 INFO  Funcotator - Initializing engine
18:11:41.515 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
18:11:41.516 INFO  Funcotator - Done initializing engine
18:11:41.516 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.516 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.516 INFO  Funcotator - Initializing data sources...
18:11:41.516 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.516 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.516 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.516 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.517 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.517 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.518 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.518 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.520 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.520 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.520 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.520 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.520 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9796238525116771195.maf
18:11:41.521 INFO  ProgressMeter - Starting traversal
18:11:41.521 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.523 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[NORMAL T*/T* AD 43,1 {AF=0.026, ALT_F1R2=0, ALT_F2R1=1, FOXOG=0.00, QSS=1450,32, REF_F1R2=29, REF_F2R1=14}],[TUMOR T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
18:11:41.523 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[NORMAL TGCGAA*/TGCGAA* AD 45,1 {AF=0.026, QSS=1503,32}],[TUMOR TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
18:11:41.524 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[NORMAL G*/G* AD 145,4 {AF=0.028, ALT_F1R2=0, ALT_F2R1=4, FOXOG=0.00, QSS=5064,124, REF_F1R2=72, REF_F2R1=73}],[TUMOR G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
18:11:41.525 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[NORMAL T*/T* AD 22,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=799,0, REF_F1R2=12, REF_F2R1=10}],[TUMOR T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
18:11:41.526 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[NORMAL A*/A* AD 45,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=1560,0, REF_F1R2=20, REF_F2R1=25}],[TUMOR A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
18:11:41.527 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[NORMAL G*/G* AD 13,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=378,0, REF_F1R2=8, REF_F2R1=5}],[TUMOR G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
18:11:41.527 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
18:11:41.527 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
18:11:41.527 WARN  Funcotator - ================================================================================
18:11:41.527 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:11:41.527 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:11:41.527 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:11:41.527 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:11:41.527 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:11:41.527 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:11:41.527 WARN  Funcotator - --------------------------------------------------------------------------------
18:11:41.527 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:11:41.527 WARN  Funcotator -  run was misconfigured.     
18:11:41.527 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:11:41.527 WARN  Funcotator - ================================================================================
18:11:41.528 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:41.528 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.593 INFO  Funcotator - ------------------------------------------------------------
18:11:41.593 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.593 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.593 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.593 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.593 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.593 INFO  Funcotator - ------------------------------------------------------------
18:11:41.594 INFO  Funcotator - ------------------------------------------------------------
18:11:41.594 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.594 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.594 INFO  Funcotator - Inflater: IntelInflater
18:11:41.594 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.594 INFO  Funcotator - Requester pays: disabled
18:11:41.594 INFO  Funcotator - Initializing engine
18:11:41.595 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
18:11:41.596 INFO  Funcotator - Done initializing engine
18:11:41.596 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.596 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.596 INFO  Funcotator - Initializing data sources...
18:11:41.596 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.596 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.596 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.596 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.596 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.596 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.596 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.596 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.597 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.597 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.597 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.597 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.598 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.599 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.600 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.600 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.600 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.601 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10831576412262131502.maf
18:11:41.601 INFO  ProgressMeter - Starting traversal
18:11:41.601 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[SM-74NEG T*/T* AD 43,1 {AF=0.026, ALT_F1R2=0, ALT_F2R1=1, FOXOG=0.00, QSS=1450,32, REF_F1R2=29, REF_F2R1=14}],[SM-74P4M T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
18:11:41.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[SM-74NEG TGCGAA*/TGCGAA* AD 45,1 {AF=0.026, QSS=1503,32}],[SM-74P4M TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
18:11:41.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[SM-74NEG G*/G* AD 145,4 {AF=0.028, ALT_F1R2=0, ALT_F2R1=4, FOXOG=0.00, QSS=5064,124, REF_F1R2=72, REF_F2R1=73}],[SM-74P4M G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
18:11:41.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[SM-74NEG T*/T* AD 22,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=799,0, REF_F1R2=12, REF_F2R1=10}],[SM-74P4M T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
18:11:41.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[SM-74NEG A*/A* AD 45,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=1560,0, REF_F1R2=20, REF_F2R1=25}],[SM-74P4M A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
18:11:41.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[SM-74NEG G*/G* AD 13,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=378,0, REF_F1R2=8, REF_F2R1=5}],[SM-74P4M G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
18:11:41.605 INFO  ProgressMeter -             unmapped              0.0                     6          90000.0
18:11:41.605 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
18:11:41.606 WARN  Funcotator - ================================================================================
18:11:41.606 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:11:41.606 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:11:41.606 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:11:41.606 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:11:41.606 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:11:41.606 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:11:41.606 WARN  Funcotator - --------------------------------------------------------------------------------
18:11:41.606 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:11:41.606 WARN  Funcotator -  run was misconfigured.     
18:11:41.606 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:11:41.606 WARN  Funcotator - ================================================================================
18:11:41.606 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:41.606 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.673 INFO  Funcotator - ------------------------------------------------------------
18:11:41.673 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.673 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.673 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.673 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.673 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.673 INFO  Funcotator - ------------------------------------------------------------
18:11:41.673 INFO  Funcotator - ------------------------------------------------------------
18:11:41.673 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.673 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.673 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.673 INFO  Funcotator - Inflater: IntelInflater
18:11:41.673 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.673 INFO  Funcotator - Requester pays: disabled
18:11:41.673 INFO  Funcotator - Initializing engine
18:11:41.674 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf
18:11:41.675 INFO  Funcotator - Done initializing engine
18:11:41.675 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.675 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.675 INFO  Funcotator - Initializing data sources...
18:11:41.675 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.675 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.676 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.676 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.676 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.677 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.677 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.679 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.679 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.680 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.680 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.680 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9954588633295326989.maf
18:11:41.680 INFO  ProgressMeter - Starting traversal
18:11:41.680 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.681 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[TUMOR T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
18:11:41.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[TUMOR TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
18:11:41.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[TUMOR G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
18:11:41.683 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[TUMOR T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
18:11:41.683 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[TUMOR A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
18:11:41.685 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[TUMOR G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
18:11:41.685 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
18:11:41.685 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
18:11:41.685 WARN  Funcotator - ================================================================================
18:11:41.685 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:11:41.685 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:11:41.685 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:11:41.685 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:11:41.685 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:11:41.685 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:11:41.685 WARN  Funcotator - --------------------------------------------------------------------------------
18:11:41.685 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:11:41.685 WARN  Funcotator -  run was misconfigured.     
18:11:41.685 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:11:41.685 WARN  Funcotator - ================================================================================
18:11:41.685 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:41.685 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.751 INFO  Funcotator - ------------------------------------------------------------
18:11:41.751 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.751 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.751 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.751 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.751 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.751 INFO  Funcotator - ------------------------------------------------------------
18:11:41.751 INFO  Funcotator - ------------------------------------------------------------
18:11:41.751 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.751 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.751 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.751 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.751 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.751 INFO  Funcotator - Inflater: IntelInflater
18:11:41.751 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.751 INFO  Funcotator - Requester pays: disabled
18:11:41.751 INFO  Funcotator - Initializing engine
18:11:41.752 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf
18:11:41.753 INFO  Funcotator - Done initializing engine
18:11:41.753 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.753 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.753 INFO  Funcotator - Initializing data sources...
18:11:41.753 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.753 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.753 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.753 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.754 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.754 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.754 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.754 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.754 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.754 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.755 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.755 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.755 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.756 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.757 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.758 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.758 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.758 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.758 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11573287769702656325.maf
18:11:41.758 INFO  ProgressMeter - Starting traversal
18:11:41.758 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[SM-74P4M T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
18:11:41.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[SM-74P4M TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
18:11:41.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[SM-74P4M G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
18:11:41.761 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[SM-74P4M T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
18:11:41.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[SM-74P4M A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
18:11:41.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[SM-74P4M G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
18:11:41.763 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
18:11:41.763 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
18:11:41.763 WARN  Funcotator - ================================================================================
18:11:41.763 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:11:41.763 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:11:41.763 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:11:41.763 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:11:41.763 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:11:41.763 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:11:41.763 WARN  Funcotator - --------------------------------------------------------------------------------
18:11:41.763 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:11:41.763 WARN  Funcotator -  run was misconfigured.     
18:11:41.763 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:11:41.763 WARN  Funcotator - ================================================================================
18:11:41.763 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:41.763 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.827 INFO  Funcotator - ------------------------------------------------------------
18:11:41.827 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.827 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.827 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.827 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.827 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.827 INFO  Funcotator - ------------------------------------------------------------
18:11:41.827 INFO  Funcotator - ------------------------------------------------------------
18:11:41.827 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.827 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.827 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.827 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.827 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.827 INFO  Funcotator - Inflater: IntelInflater
18:11:41.827 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.827 INFO  Funcotator - Requester pays: disabled
18:11:41.827 INFO  Funcotator - Initializing engine
18:11:41.828 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:11:41.829 INFO  Funcotator - Done initializing engine
18:11:41.829 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.829 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.829 INFO  Funcotator - Initializing data sources...
18:11:41.829 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.829 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.830 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.830 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.830 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.831 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.831 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.831 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.832 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.833 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.834 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.834 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.834 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.834 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3600649287754677542.vcf
18:11:41.838 INFO  ProgressMeter - Starting traversal
18:11:41.838 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:41.848 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
18:11:41.848 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:11:41.848 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:11:41.850 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.851 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3600649287754677542.vcf
18:11:41.916 INFO  Funcotator - ------------------------------------------------------------
18:11:41.916 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.916 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.916 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.916 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.916 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.916 INFO  Funcotator - ------------------------------------------------------------
18:11:41.916 INFO  Funcotator - ------------------------------------------------------------
18:11:41.916 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.916 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.916 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.917 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.917 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.917 INFO  Funcotator - Inflater: IntelInflater
18:11:41.917 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.917 INFO  Funcotator - Requester pays: disabled
18:11:41.917 INFO  Funcotator - Initializing engine
18:11:41.917 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
18:11:41.918 INFO  Funcotator - Done initializing engine
18:11:41.918 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.918 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.918 INFO  Funcotator - Initializing data sources...
18:11:41.918 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.918 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.919 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.919 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:41.919 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:41.920 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:41.920 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.920 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:41.920 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.921 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.922 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:41.923 INFO  Funcotator - Initializing Funcotator Engine...
18:11:41.923 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:41.923 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:41.923 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out2337210751560216024.maf
18:11:41.924 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:41.924 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:41.984 INFO  Funcotator - ------------------------------------------------------------
18:11:41.984 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:41.984 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:41.984 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:41.984 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:41.984 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:41 PM UTC
18:11:41.984 INFO  Funcotator - ------------------------------------------------------------
18:11:41.984 INFO  Funcotator - ------------------------------------------------------------
18:11:41.984 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:41.984 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:41.984 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:41.984 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:41.984 INFO  Funcotator - Deflater: IntelDeflater
18:11:41.984 INFO  Funcotator - Inflater: IntelInflater
18:11:41.984 INFO  Funcotator - GCS max retries/reopens: 20
18:11:41.984 INFO  Funcotator - Requester pays: disabled
18:11:41.984 INFO  Funcotator - Initializing engine
18:11:41.985 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
18:11:41.998 INFO  Funcotator - Done initializing engine
18:11:41.998 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:41.998 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:41.998 INFO  Funcotator - Initializing data sources...
18:11:41.999 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:41.999 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:41.999 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:41.999 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:41.999 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:41.999 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:41.999 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:41.999 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:42.000 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:11:42.000 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:11:42.000 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:42.000 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:42.001 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:42.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:42.016 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:11:42.024 INFO  Funcotator - Initializing Funcotator Engine...
18:11:42.028 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:42.028 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14010857729732410895.maf
18:11:42.029 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:42.029 INFO  ProgressMeter - Starting traversal
18:11:42.029 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:42.031 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
18:11:42.031 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
18:11:42.032 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.032 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:42.032 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
18:11:42.032 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
18:11:42.033 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199000 Q308.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-1.052e+00, ClippingRankSum=-1.910e-01, DP=82, ExcessHet=4.7712, FS=24.798, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=34.33, MQRankSum=-2.200e+00, QD=6.43, ReadPosRankSum=-9.570e-01, SOR=2.422, VQSLOD=-1.252e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:13,0,0:13:0:.:.:0,0,146,0,146,146	0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886	0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.036 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.036 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:42.037 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
18:11:42.037 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
18:11:42.037 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199001 Q308.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-1.339e+00, ClippingRankSum=0.00, DP=82, ExcessHet=4.7712, FS=24.798, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=34.33, MQRankSum=-2.200e+00, QD=6.43, ReadPosRankSum=-1.148e+00, SOR=2.422, VQSLOD=-1.254e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:13,0,0:13:0:.:.:0,0,146,0,146,146	0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886	0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.037 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
18:11:42.037 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
18:11:42.037 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.037 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:42.038 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
18:11:42.038 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
18:11:42.038 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199002 Q194.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-2.991e+00, ClippingRankSum=-4.900e-02, DP=106, ExcessHet=4.7712, FS=16.473, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=37.30, MQRankSum=-1.470e-01, QD=2.95, ReadPosRankSum=-7.360e-01, SOR=1.435, VQSLOD=-9.044e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:15,0,0:15:0:.:.:0,0,273,0,273,273	0/1:23,7,0:30:49:.:.:49,0,658,118,678,796	0/2:30,0,6:36:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:160,252,1513,0,1261,1243 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.038 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
18:11:42.038 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
18:11:42.038 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
18:11:42.038 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
18:11:42.039 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
18:11:42.039 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
18:11:42.039 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199003 Q1706.05 of type=SNP alleles=[G*, *, A] attr={AC=[2, 2], AF=[0.500, 0.500], AN=4, DB=true, DP=76, ExcessHet=3.0103, FS=0.000, MLEAC=[2, 2], MLEAF=[0.500, 0.500], MQ=34.51, POSITIVE_TRAIN_SITE=true, QD=32.87, SOR=0.968, VQSLOD=-7.669e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,24,0:24:75:1|1:908920_C_G:1104,75,0,1104,75,1104	./.:33,0,0:33:.:.:.:0,0,0,0,0,0	2/2:0,0,15:15:45:1|1:908920_C_G:627,627,627,45,45,0 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.039 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.039 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:42.040 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
18:11:42.040 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
18:11:42.040 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199004 Q1368.97 of type=SNP alleles=[A*, *, G] attr={AC=[2, 1], AF=[0.500, 0.250], AN=4, DB=true, DP=67, ExcessHet=3.0103, FS=0.000, MLEAC=[2, 1], MLEAF=[0.500, 0.250], MQ=32.71, QD=28.53, SOR=0.302, VQSLOD=-9.124e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,18,0:18:54:1|1:908920_C_G:810,54,0,810,54,810	./.:29,0,0:29:.:.:.:0,0,0,0,0,0	0/2:1,0,15:16:59:0|1:908920_C_G:579,582,687,0,105,59 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.040 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.040 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:42.040 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
18:11:42.041 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
18:11:42.041 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199005 Q1434.91 of type=SNP alleles=[A*, *, G] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=0.533, ClippingRankSum=1.60, DB=true, DP=88, ExcessHet=3.9794, FS=0.000, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=49.95, MQRankSum=1.07, NEGATIVE_TRAIN_SITE=true, QD=27.59, ReadPosRankSum=2.40, SOR=0.902, VQSLOD=-9.887e-01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:5,9,0:14:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:264,0,168,283,195,478	0/1:7,8,0:15:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:206,0,264,233,288,521	2/2:0,0,23:23:71:.:.:990,990,990,71,71,0 filters=
18:11:42.041 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
18:11:42.041 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
18:11:42.041 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
18:11:42.041 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:42.042 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
18:11:42.042 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
18:11:42.042 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199006 Q2248.91 of type=SNP alleles=[T*, *, C] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=-9.740e-01, ClippingRankSum=0.545, DB=true, DP=101, ExcessHet=3.9794, FS=6.882, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=49.59, MQRankSum=-1.490e-01, NEGATIVE_TRAIN_SITE=true, QD=23.18, ReadPosRankSum=0.578, SOR=1.028, VQSLOD=-8.789e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:18,17,0:35:99:456,0,705,510,756,1266	0/1:15,17,0:32:99:467,0,579,512,630,1142	2/2:0,0,30:30:91:1351,1351,1351,91,91,0 filters=
18:11:42.042 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
18:11:42.042 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
18:11:42.042 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.042 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:42.043 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
18:11:42.043 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
18:11:42.043 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199007 Q1821.97 of type=SNP alleles=[A*, *, G] attr={AC=[2, 1], AF=[0.500, 0.250], AN=4, DB=true, DP=92, ExcessHet=3.0103, FS=10.616, MLEAC=[2, 1], MLEAF=[0.500, 0.250], MQ=32.68, POSITIVE_TRAIN_SITE=true, QD=27.61, SOR=1.479, VQSLOD=-1.050e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	./.:21,0,0:21:.:.:.:0,0,0,0,0,0	1/1:0,31,0:31:96:1|1:996335_C_A:1103,96,0,1103,96,1103	0/2:11,0,24:35:99:.:.:739,773,1159,0,386,316 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.043 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
18:11:42.043 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
18:11:42.043 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
18:11:42.043 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
18:11:42.044 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199008 Q601.66 of type=SNP alleles=[T*, *, C] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=-5.100e-01, ClippingRankSum=1.36, DB=true, DP=95, ExcessHet=3.9794, FS=27.935, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=48.12, MQRankSum=1.08, NEGATIVE_TRAIN_SITE=true, QD=12.53, ReadPosRankSum=0.849, SOR=2.062, VQSLOD=-3.093e+00, culprit=FS} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:11,7,0:18:88:0|1:1611567_CT_C:88,0,187,121,208,329	2/2:1,0,12:13:16:.:.:212,216,235,16,35,0	0/1:4,13,0:17:20:0|1:1611567_CT_C:327,0,20,339,58,397 filters=VQSRTrancheSNP99.90to100.00+
18:11:42.044 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
18:11:42.044 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
18:11:42.044 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
18:11:42.044 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
18:11:42.044 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
18:11:42.044 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
18:11:42.045 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199009 Q469.89 of type=SNP alleles=[A*, *, G] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=2.60, ClippingRankSum=1.32, DB=true, DP=80, ExcessHet=3.9794, FS=2.173, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=53.43, MQRankSum=1.82, NEGATIVE_TRAIN_SITE=true, QD=6.44, ReadPosRankSum=1.70, SOR=1.002, VQSLOD=-6.972e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:33,7,0:40:84:84,0,865,180,886,1065	2/2:0,0,9:9:27:332,332,332,27,27,0	0/1:18,6,0:24:79:79,0,466,133,483,616 filters=
18:11:42.045 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
18:11:42.045 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
18:11:42.045 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
18:11:42.045 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
[May 27, 2025 at 6:11:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:42.180 INFO  Funcotator - ------------------------------------------------------------
18:11:42.180 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:42.180 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:42.180 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:42.180 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:42.180 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:42 PM UTC
18:11:42.180 INFO  Funcotator - ------------------------------------------------------------
18:11:42.180 INFO  Funcotator - ------------------------------------------------------------
18:11:42.180 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:42.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:42.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:42.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:42.180 INFO  Funcotator - Deflater: IntelDeflater
18:11:42.180 INFO  Funcotator - Inflater: IntelInflater
18:11:42.180 INFO  Funcotator - GCS max retries/reopens: 20
18:11:42.180 INFO  Funcotator - Requester pays: disabled
18:11:42.180 INFO  Funcotator - Initializing engine
18:11:42.181 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
18:11:42.182 INFO  Funcotator - Done initializing engine
18:11:42.182 INFO  Funcotator - Validating sequence dictionaries...
18:11:42.183 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2663383040
18:11:42.244 INFO  Funcotator - ------------------------------------------------------------
18:11:42.244 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:42.244 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:42.244 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:42.244 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:42.244 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:42 PM UTC
18:11:42.244 INFO  Funcotator - ------------------------------------------------------------
18:11:42.244 INFO  Funcotator - ------------------------------------------------------------
18:11:42.244 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:42.244 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:42.244 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:42.244 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:42.244 INFO  Funcotator - Deflater: IntelDeflater
18:11:42.244 INFO  Funcotator - Inflater: IntelInflater
18:11:42.244 INFO  Funcotator - GCS max retries/reopens: 20
18:11:42.244 INFO  Funcotator - Requester pays: disabled
18:11:42.244 INFO  Funcotator - Initializing engine
18:11:42.246 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
18:11:42.246 INFO  Funcotator - Done initializing engine
18:11:42.247 INFO  Funcotator - Validating sequence dictionaries...
18:11:42.247 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:42.247 INFO  Funcotator - Initializing data sources...
18:11:42.247 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:42.247 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:42.247 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:42.247 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:42.247 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:42.247 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:42.248 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:42.249 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:42.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:42.338 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:42.360 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:42.368 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:42.368 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:42.369 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:42.369 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:43.015 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:43.053 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:43.053 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:43.054 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:43.054 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:43.143 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:43.143 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:43.144 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:43.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:43.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:43.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:43.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:43.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:43.184 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:43.185 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:43.187 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:43.190 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:43.192 INFO  Funcotator - Initializing Funcotator Engine...
18:11:43.192 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:43.192 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:43.192 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator9393893960546941405.vcf
18:11:43.194 INFO  ProgressMeter - Starting traversal
18:11:43.194 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:45.356 INFO  ProgressMeter -             unmapped              0.0                   198           5494.9
18:11:45.356 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:11:45.356 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:11:45.365 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3001024512
18:11:45.429 INFO  Funcotator - ------------------------------------------------------------
18:11:45.429 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:45.429 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:45.429 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:45.429 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:45.429 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:45 PM UTC
18:11:45.429 INFO  Funcotator - ------------------------------------------------------------
18:11:45.429 INFO  Funcotator - ------------------------------------------------------------
18:11:45.429 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:45.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:45.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:45.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:45.429 INFO  Funcotator - Deflater: IntelDeflater
18:11:45.429 INFO  Funcotator - Inflater: IntelInflater
18:11:45.429 INFO  Funcotator - GCS max retries/reopens: 20
18:11:45.429 INFO  Funcotator - Requester pays: disabled
18:11:45.429 INFO  Funcotator - Initializing engine
18:11:45.431 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
18:11:45.432 INFO  Funcotator - Done initializing engine
18:11:45.432 INFO  Funcotator - Validating sequence dictionaries...
18:11:45.432 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:45.432 INFO  Funcotator - Initializing data sources...
18:11:45.432 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:45.432 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:45.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:45.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:45.434 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:45.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:45.435 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:45.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:45.497 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:45.504 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:45.504 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:45.504 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:45.504 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:46.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:46.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:46.127 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:46.127 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:46.128 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:46.210 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:46.210 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:46.211 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:46.238 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:46.238 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:46.238 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:46.239 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:46.239 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:46.239 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:46.240 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:46.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:46.244 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:46.246 INFO  Funcotator - Initializing Funcotator Engine...
18:11:46.246 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
18:11:46.246 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:46.246 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator13420658000849683379.maf
18:11:46.247 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:46.247 INFO  ProgressMeter - Starting traversal
18:11:46.247 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:48.339 INFO  ProgressMeter -             unmapped              0.0                   198           5681.5
18:11:48.339 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
18:11:48.339 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
18:11:48.339 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:48 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3045064704
18:11:48.406 INFO  Funcotator - ------------------------------------------------------------
18:11:48.406 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:48.406 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:48.406 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:48.406 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:48.406 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:48 PM UTC
18:11:48.406 INFO  Funcotator - ------------------------------------------------------------
18:11:48.406 INFO  Funcotator - ------------------------------------------------------------
18:11:48.406 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:48.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:48.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:48.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:48.406 INFO  Funcotator - Deflater: IntelDeflater
18:11:48.406 INFO  Funcotator - Inflater: IntelInflater
18:11:48.406 INFO  Funcotator - GCS max retries/reopens: 20
18:11:48.406 INFO  Funcotator - Requester pays: disabled
18:11:48.406 INFO  Funcotator - Initializing engine
18:11:48.433 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
18:11:48.454 INFO  Funcotator - Done initializing engine
18:11:48.454 INFO  Funcotator - Validating sequence dictionaries...
18:11:48.461 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:48.461 INFO  Funcotator - Initializing data sources...
18:11:48.461 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:48.461 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:48.461 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:48.461 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:48.461 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:48.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:48.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:48.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:48.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:48.463 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:48.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
18:11:48.505 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
18:11:48.524 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
18:11:48.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
18:11:48.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
18:11:48.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
18:11:48.532 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v90_38.hg38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
18:11:49.105 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
18:11:49.170 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:49.170 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.171 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
18:11:49.171 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
18:11:49.172 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
18:11:49.173 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:49.173 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:49.173 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:49.174 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:49.175 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:49.176 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
18:11:49.178 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.181 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:49.181 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator9813113002395774587.vcf
18:11:49.182 INFO  ProgressMeter - Starting traversal
18:11:49.182 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.187 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
18:11:49.190 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3045064704
18:11:49.257 INFO  Funcotator - ------------------------------------------------------------
18:11:49.257 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.257 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.257 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.257 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.257 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.257 INFO  Funcotator - ------------------------------------------------------------
18:11:49.257 INFO  Funcotator - ------------------------------------------------------------
18:11:49.257 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.257 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.257 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.257 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.257 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.257 INFO  Funcotator - Inflater: IntelInflater
18:11:49.257 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.257 INFO  Funcotator - Requester pays: disabled
18:11:49.257 INFO  Funcotator - Initializing engine
18:11:49.260 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
18:11:49.260 INFO  Funcotator - Done initializing engine
18:11:49.260 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.260 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.260 INFO  Funcotator - Initializing data sources...
18:11:49.260 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
18:11:49.260 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.repro.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
18:11:49.260 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.260 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.261 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.261 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.261 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.repro.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
18:11:49.261 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
18:11:49.262 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
18:11:49.262 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.repro.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
18:11:49.263 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
18:11:49.263 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.263 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.263 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.263 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.263 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing9891560433789588924.vcf
18:11:49.264 INFO  ProgressMeter - Starting traversal
18:11:49.264 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.268 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
18:11:49.268 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:11:49.268 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
18:11:49.270 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.271 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing9891560433789588924.vcf
18:11:49.334 INFO  Funcotator - ------------------------------------------------------------
18:11:49.334 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.334 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.334 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.334 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.334 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.334 INFO  Funcotator - ------------------------------------------------------------
18:11:49.334 INFO  Funcotator - ------------------------------------------------------------
18:11:49.334 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.334 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.334 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.334 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.334 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.334 INFO  Funcotator - Inflater: IntelInflater
18:11:49.334 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.334 INFO  Funcotator - Requester pays: disabled
18:11:49.334 INFO  Funcotator - Initializing engine
18:11:49.335 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:11:49.336 INFO  Funcotator - Done initializing engine
18:11:49.336 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.336 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.336 INFO  Funcotator - Initializing data sources...
18:11:49.336 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.336 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.336 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.337 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.337 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.337 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.338 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.338 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.338 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.339 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.340 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.341 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.341 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.341 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.341 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12115714311096080930.maf
18:11:49.341 INFO  ProgressMeter - Starting traversal
18:11:49.341 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.344 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178872355 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.823, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178872355, ILLUMINA_STRAND=TOP, N_AA=4, N_AB=194, N_BB=1053, PROBE_A=AATGTGTTACAATCTGTCCCCCACCATATACATATACAAAGTAGCAGTCC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.02, devTHETA_AB=0.035, devTHETA_BB=0.018, devX_AA=0.095, devX_AB=0.05, devX_BB=0.02, devY_AA=0.022, devY_AB=0.06, devY_BB=0.094, meanR_AA=0.748, meanR_AB=0.789, meanR_BB=0.755, meanTHETA_AA=0.052, meanTHETA_AB=0.569, meanTHETA_BB=0.946, meanX_AA=0.692, meanX_AB=0.352, meanX_BB=0.059, meanY_AA=0.056, meanY_AB=0.437, meanY_BB=0.695, refSNP=rs11706842, zthresh_X=0.18402316111, zthresh_Y=0.185250013887} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.514, GTA=1/0, GTZ=1/0, IGC=0.849, LRR=-0.05, NORMX=0.333, NORMY=0.428, R=0.761, THETA=0.579, X=4554, Y=2131}]] filters=
18:11:49.345 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178902506 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=928, GC_SCORE=0.893, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178902506, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=28, N_BB=1220, PROBE_A=TTATTGGACCAGCCTAGACTGAAAATCTTCTGTTTAGGCATTTTGGTGGG, PROBE_B=., SOURCE=psych, devR_AA=0.1, devR_AB=0.105, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.023, devTHETA_BB=0.01, devX_AA=0.101, devX_AB=0.054, devX_BB=0.015, devY_AA=0.031, devY_AB=0.055, devY_BB=0.097, meanR_AA=0.948, meanR_AB=1.181, meanR_BB=0.994, meanTHETA_AA=0.026, meanTHETA_AB=0.512, meanTHETA_BB=0.973, meanX_AA=0.911, meanX_AB=0.58, meanX_BB=0.041, meanY_AA=0.037, meanY_AB=0.602, meanY_BB=0.953, refSNP=rs111868222, zthresh_X=0.140378981558, zthresh_Y=0.166929562077} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.99, GTA=0/0, GTZ=0/0, IGC=0.882, LRR=0.069, NORMX=0.057, NORMY=0.99, R=1.047, THETA=0.963, X=1498, Y=5593}]] filters=
18:11:49.345 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178907849 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.797, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178907849, ILLUMINA_STRAND=TOP, N_AA=19, N_AB=360, N_BB=872, PROBE_A=GAGGCCCTAACTGGGGCCCAGAAAATTGTACTGAAGGATACTTGCTTCCT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.023, devTHETA_AB=0.038, devTHETA_BB=0.021, devX_AA=0.094, devX_AB=0.05, devX_BB=0.018, devY_AA=0.019, devY_AB=0.056, devY_BB=0.093, meanR_AA=0.556, meanR_AB=0.58, meanR_BB=0.576, meanTHETA_AA=0.054, meanTHETA_AB=0.544, meanTHETA_BB=0.94, meanX_AA=0.513, meanX_AB=0.27, meanX_BB=0.05, meanY_AA=0.043, meanY_AB=0.31, meanY_BB=0.526, refSNP=rs9866361, zthresh_X=0.161949964118, zthresh_Y=0.175918019742} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.978, GTA=0/0, GTZ=0/0, IGC=0.811, LRR=-0.054, NORMX=0.061, NORMY=0.495, R=0.555, THETA=0.922, X=1038, Y=2429}]] filters=
18:11:49.345 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916753 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.886, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916753, ILLUMINA_STRAND=TOP, N_AA=1247, N_AB=0, N_BB=0, PROBE_A=GATAGTGACTTTAGAATGCCTCCGTGAGGCTACATTAATAACCATAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.094, devX_AB=0.05, devX_BB=0.017, devY_AA=0.015, devY_AB=0.052, devY_BB=0.098, meanR_AA=0.455, meanR_AB=0.541, meanR_BB=0.503, meanTHETA_AA=0.047, meanTHETA_AB=0.511, meanTHETA_BB=0.976, meanX_AA=0.424, meanX_AB=0.266, meanX_BB=0.018, meanY_AA=0.031, meanY_AB=0.275, meanY_BB=0.485, refSNP=rs190372148, zthresh_X=0.182850738152, zthresh_Y=0.12847847542} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.489, LRR=0.114, NORMX=0.459, NORMY=0.034, R=0.493, THETA=0.047, X=8065, Y=228}]] filters=
18:11:49.346 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916791 Q. of type=SNP alleles=[C*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.89, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916791, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TAACCATAAAGCATGAACTATTTAAAGAAGCAAGAAAATACCCCCTCCAT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.013, devX_AA=0.099, devX_AB=0.053, devX_BB=0.014, devY_AA=0.024, devY_AB=0.052, devY_BB=0.096, meanR_AA=0.738, meanR_AB=0.886, meanR_BB=0.745, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.965, meanX_AA=0.711, meanX_AB=0.447, meanX_BB=0.039, meanY_AA=0.027, meanY_AB=0.439, meanY_BB=0.706, refSNP=rs71310379, zthresh_X=0.133750336661, zthresh_Y=0.164321280546} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.494, LRR=0.001, NORMX=0.022, NORMY=0.718, R=0.741, THETA=0.98, X=620, Y=4057}]] filters=
18:11:49.346 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178921158 Q. of type=SNP alleles=[G*, A] attr={AC=1, AF=0.500, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.788, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178921158, ILLUMINA_STRAND=TOP, N_AA=30, N_AB=414, N_BB=807, PROBE_A=CTTTCGTGCAATTTATATTCAGAAGTGTTTGATTGATCTTGTGCTTCAAC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.016, devTHETA_AB=0.029, devTHETA_BB=0.015, devX_AA=0.094, devX_AB=0.049, devX_BB=0.021, devY_AA=0.019, devY_AB=0.061, devY_BB=0.092, meanR_AA=0.827, meanR_AB=0.983, meanR_BB=0.947, meanTHETA_AA=0.05, meanTHETA_AB=0.585, meanTHETA_BB=0.933, meanX_AA=0.767, meanX_AB=0.426, meanX_BB=0.09, meanY_AA=0.06, meanY_AB=0.557, meanY_BB=0.857, refSNP=rs7623154, zthresh_X=0.224662521322, zthresh_Y=0.204527740428} GT=[[0816201804HC0_R01C01 G*/A {BAF=0.484, GTA=1/0, GTZ=1/0, IGC=0.797, LRR=0.017, NORMX=0.442, NORMY=0.547, R=0.99, THETA=0.567, X=6004, Y=2730}]] filters=
18:11:49.347 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 Q. of type=SNP alleles=[C*, G] attr={AC=0, AF=0.00, ALLELE_A=G, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178922361, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1249, PROBE_A=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACG, PROBE_B=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACC, SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.014, devX_AA=0.099, devX_AB=0.052, devX_BB=0.014, devY_AA=0.022, devY_AB=0.052, devY_BB=0.097, meanR_AA=0.664, meanR_AB=0.793, meanR_BB=0.678, meanTHETA_AA=0.024, meanTHETA_AB=0.501, meanTHETA_BB=0.977, meanX_AA=0.64, meanX_AB=0.396, meanX_BB=0.024, meanY_AA=0.025, meanY_AB=0.397, meanY_BB=0.654, refSNP=rs113613074, zthresh_X=0.119568794798, zthresh_Y=0.156845592246} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.515, LRR=-0.048, NORMX=0.015, NORMY=0.639, R=0.654, THETA=0.986, X=603, Y=11188}]] filters=
18:11:49.347 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=1161, GC_SCORE=0.868, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178927410, ILLUMINA_STRAND=BOT, N_AA=1072, N_AB=169, N_BB=0, PROBE_A=GAGCAAATGGAAAGGCAAAGTCGAGCAGCACGAGGAAGATCAGGAATGTA, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.042, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.058, devX_BB=0.024, devY_AA=0.015, devY_AB=0.059, devY_BB=0.099, meanR_AA=0.829, meanR_AB=0.918, meanR_BB=0.742, meanTHETA_AA=0.017, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=0.808, meanX_AB=0.452, meanX_BB=0.028, meanY_AA=0.021, meanY_AB=0.466, meanY_BB=0.714, refSNP=rs2230461, zthresh_X=0.183044318831, zthresh_Y=0.127662818665} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.009, GTA=0/0, GTZ=0/0, IGC=0.851, LRR=0.267, NORMX=0.961, NORMY=0.038, R=1, THETA=0.025, X=15373, Y=361}]] filters=
18:11:49.347 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=971, GC_SCORE=0.869, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178932551, ILLUMINA_STRAND=TOP, N_AA=343, N_AB=398, N_BB=479, PROBE_A=GTGAAGACCTGCTGTTTTCTCTGCTTCCAAGCTCAACTAACAATATATTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.131, devR_AB=0.1, devR_BB=0.123, devTHETA_AA=0.017, devTHETA_AB=0.023, devTHETA_BB=0.022, devX_AA=0.126, devX_AB=0.061, devX_BB=0.024, devY_AA=0.017, devY_AB=0.074, devY_BB=0.118, meanR_AA=0.622, meanR_AB=0.938, meanR_BB=0.739, meanTHETA_AA=0.028, meanTHETA_AB=0.563, meanTHETA_BB=0.965, meanX_AA=0.596, meanX_AB=0.423, meanX_BB=0.038, meanY_AA=0.026, meanY_AB=0.515, meanY_BB=0.701, refSNP=rs12494623, zthresh_X=0.152176899827, zthresh_Y=0.170103096568} GT=[[0816201804HC0_R01C01 T/T {BAF=0.027, GTA=1/1, GTZ=1/1, IGC=0.906, LRR=-0.336, NORMX=0.465, NORMY=0.042, R=0.507, THETA=0.057, X=7174, Y=362}]] filters=
18:11:49.348 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.891, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178937400, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CATACACAGATGTATTGCTTGGTAAAAGATTGGCCTCCAATCAAACCTGA, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.108, devR_BB=0.1, devTHETA_AA=0.013, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.053, devX_BB=0.026, devY_AA=0.015, devY_AB=0.053, devY_BB=0.1, meanR_AA=0.79, meanR_AB=0.96, meanR_BB=0.803, meanTHETA_AA=0.031, meanTHETA_AB=0.503, meanTHETA_BB=0.976, meanX_AA=0.753, meanX_AB=0.477, meanX_BB=0.029, meanY_AA=0.037, meanY_AB=0.482, meanY_BB=0.773, refSNP=rs137902538, zthresh_X=0.187164813479, zthresh_Y=0.140282002247} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.496, LRR=-0.05, NORMX=0.731, NORMY=0.031, R=0.761, THETA=0.027, X=12748, Y=231}]] filters=
18:11:49.348 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.902, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178947118, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=ACCTTTCAAGCCGCCTTTGCACTGAATTTGCATAATAGTGTGAGAATTTC, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.098, devX_AB=0.052, devX_BB=0.014, devY_AA=0.019, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.576, meanR_AB=0.681, meanR_BB=0.596, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.964, meanX_AA=0.555, meanX_AB=0.344, meanX_BB=0.032, meanY_AA=0.021, meanY_AB=0.337, meanY_BB=0.565, zthresh_X=0.122228724787, zthresh_Y=0.159007429626} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.509, LRR=0.03, NORMX=0.022, NORMY=0.585, R=0.607, THETA=0.977, X=711, Y=3117}]] filters=
18:11:49.349 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.848, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178950297, ILLUMINA_STRAND=BOT, N_AA=486, N_AB=560, N_BB=205, PROBE_A=GTCTGTGTGTCTGCTTTTGTGTGTATCTGCTGTTTTGGTAATTATAGTTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.102, devR_AB=0.12, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.028, devTHETA_BB=0.016, devX_AA=0.099, devX_AB=0.057, devX_BB=0.022, devY_AA=0.018, devY_AB=0.057, devY_BB=0.094, meanR_AA=1.064, meanR_AB=1.186, meanR_BB=1.006, meanTHETA_AA=0.03, meanTHETA_AB=0.494, meanTHETA_BB=0.943, meanX_AA=1.016, meanX_AB=0.598, meanX_BB=0.083, meanY_AA=0.048, meanY_AB=0.587, meanY_BB=0.923, refSNP=rs1607237, zthresh_X=0.199217026256, zthresh_Y=0.172626912202} GT=[[0816201804HC0_R01C01 T/T {BAF=0, GTA=1/1, GTZ=1/1, IGC=0.882, LRR=-0.014, NORMX=1.013, NORMY=0.039, R=1.052, THETA=0.025, X=13288, Y=291}]] filters=
18:11:49.349 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.832, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960744, ILLUMINA_STRAND=BOT, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=AAGATTTCTCTGCTCTTCCTTTGCTCCTCCTCATAATGCACAGTTTGAAC, PROBE_B=., SOURCE=1000_genomes, devR_AA=0.1, devR_AB=0.195, devR_BB=0.113, devTHETA_AA=0.007, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.059, devX_BB=0.042, devY_AA=0.015, devY_AB=0.058, devY_BB=0.117, meanR_AA=1.388, meanR_AB=1.725, meanR_BB=1.296, meanTHETA_AA=0.014, meanTHETA_AB=0.495, meanTHETA_BB=0.975, meanX_AA=1.358, meanX_AB=0.87, meanX_BB=0.048, meanY_AA=0.029, meanY_AB=0.855, meanY_BB=1.248, refSNP=rs200646413, zthresh_X=0.181538312311, zthresh_Y=0.124907131052} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0.004, GTA=0/0, GTZ=0/0, IGC=0.423, LRR=0.033, NORMX=1.384, NORMY=0.039, R=1.423, THETA=0.018, X=24000, Y=330}]] filters=
18:11:49.349 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.847, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960843, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.18, devR_BB=0.106, devTHETA_AA=0.009, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.057, devX_BB=0.04, devY_AA=0.017, devY_AB=0.058, devY_BB=0.11, meanR_AA=1.287, meanR_AB=1.594, meanR_BB=1.215, meanTHETA_AA=0.034, meanTHETA_AB=0.505, meanTHETA_BB=0.976, meanX_AA=1.221, meanX_AB=0.791, meanX_BB=0.044, meanY_AA=0.066, meanY_AB=0.804, meanY_BB=1.171, refSNP=rs145985409, zthresh_X=0.19811140407, zthresh_Y=0.172079887333} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.01, GTA=0/0, GTZ=0/0, IGC=0.441, LRR=0.077, NORMX=1.276, NORMY=0.087, R=1.363, THETA=0.043, X=22154, Y=590}]] filters=
18:11:49.349 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.901, ILLUMINA_BUILD=37.2, ILLUMINA_CHR=3, ILLUMINA_POS=178962380, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=CGACTGGCTGGACTGTGCCTTCACCTGTGGTGTGCACTGCCACGGTCAGG, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.133, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.009, devX_AA=0.101, devX_AB=0.054, devX_BB=0.013, devY_AA=0.032, devY_AB=0.054, devY_BB=0.097, meanR_AA=0.964, meanR_AB=1.179, meanR_BB=0.948, meanTHETA_AA=0.024, meanTHETA_AB=0.5, meanTHETA_BB=0.976, meanX_AA=0.928, meanX_AB=0.589, meanX_BB=0.034, meanY_AA=0.036, meanY_AB=0.59, meanY_BB=0.915, refSNP=rs199686819, zthresh_X=0.12173904259, zthresh_Y=0.159179424244} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.508, LRR=-0.062, NORMX=0.033, NORMY=0.876, R=0.909, THETA=0.976, X=819, Y=4947}]] filters=
18:11:49.350 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.879, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178962425, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=GAGAGAAGAATCGACCTGCACTGCCATCCACACAGATATCATGGACGACT, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.121, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.011, devX_AA=0.101, devX_AB=0.054, devX_BB=0.014, devY_AA=0.029, devY_AB=0.053, devY_BB=0.095, meanR_AA=0.883, meanR_AB=1.074, meanR_BB=0.877, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.851, meanX_AB=0.543, meanX_BB=0.048, meanY_AA=0.032, meanY_AB=0.532, meanY_BB=0.829, refSNP=rs145138176, zthresh_X=0.14237441016, zthresh_Y=0.168724424863} GT=[[0816201804HC0_R01C01 C*/C* {BAF=0.999, GTA=0/0, GTZ=0/0, IGC=0.48, LRR=-0.121, NORMX=0.045, NORMY=0.761, R=0.806, THETA=0.963, X=1125, Y=4047}]] filters=
18:11:49.350 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968543 Q. of type=SNP alleles=[G*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968543, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=1, N_BB=1250, PROBE_A=GGGCTTCTCAGTCCTAATGTTCTTCTTGCTCGGAACAACCATTCTAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.104, devR_AB=0.156, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.008, devX_AA=0.107, devX_AB=0.058, devX_BB=0.014, devY_AA=0.036, devY_AB=0.057, devY_BB=0.097, meanR_AA=1.1, meanR_AB=1.381, meanR_BB=1.127, meanTHETA_AA=0.025, meanTHETA_AB=0.492, meanTHETA_BB=0.975, meanX_AA=1.059, meanX_AB=0.7, meanX_BB=0.042, meanY_AA=0.041, meanY_AB=0.682, meanY_BB=1.085, refSNP=rs61734056, zthresh_X=0.135160960006, zthresh_Y=0.165299195841} GT=[[0816201804HC0_R01C01 G*/G* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.897, LRR=0.034, NORMX=0.04, NORMY=1.113, R=1.153, THETA=0.977, X=972, Y=6285}]] filters=
18:11:49.350 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968568 Q. of type=SNP alleles=[A*, C] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=C, AN=2, BEADSET_ID=1168, GC_SCORE=0.889, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968568, ILLUMINA_STRAND=BOT, N_AA=1249, N_AB=1, N_BB=0, PROBE_A=CCGTGATGCTGGGGTTTGCCATGATGGGCTTCTCAGTCCTAATGTTCTTC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.143, devR_AB=0.175, devR_BB=0.109, devTHETA_AA=0.01, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.14, devX_AB=0.076, devX_BB=0.041, devY_AA=0.016, devY_AB=0.077, devY_BB=0.113, meanR_AA=1.113, meanR_AB=1.547, meanR_BB=1.25, meanTHETA_AA=0.019, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=1.081, meanX_AB=0.763, meanX_BB=0.046, meanY_AA=0.032, meanY_AB=0.784, meanY_BB=1.204, refSNP=rs2276802, zthresh_X=0.189602852188, zthresh_Y=0.145988814983} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.878, LRR=-0.023, NORMX=1.069, NORMY=0.021, R=1.089, THETA=0.012, X=17958, Y=362}]] filters=
18:11:49.350 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968634 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.885, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968634, ILLUMINA_STRAND=TOP, N_AA=216, N_AB=596, N_BB=439, PROBE_A=ACTACAGTGATGGAGACCCACTAGATGTGCACAAGAGGCTGCCATCCAGT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.011, devTHETA_AB=0.025, devTHETA_BB=0.01, devX_AA=0.096, devX_AB=0.058, devX_BB=0.015, devY_AA=0.019, devY_AB=0.054, devY_BB=0.097, meanR_AA=1.156, meanR_AB=1.266, meanR_BB=0.992, meanTHETA_AA=0.036, meanTHETA_AB=0.47, meanTHETA_BB=0.972, meanX_AA=1.094, meanX_AB=0.662, meanX_BB=0.042, meanY_AA=0.062, meanY_AB=0.603, meanY_BB=0.951, refSNP=rs7645550, zthresh_X=0.139062088415, zthresh_Y=0.166539592425} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.496, GTA=1/0, GTZ=1/0, IGC=0.922, LRR=-0.041, NORMX=0.647, NORMY=0.582, R=1.23, THETA=0.466, X=11372, Y=3338}]] filters=
18:11:49.351 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968660 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.862, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968660, ILLUMINA_STRAND=TOP, N_AA=987, N_AB=246, N_BB=18, PROBE_A=TGCCTCAGGGAAGAAGAGAGAGACAGACTACAGTGATGGAGACCCACTAG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.01, devTHETA_AB=0.039, devTHETA_BB=0.016, devX_AA=0.096, devX_AB=0.061, devX_BB=0.022, devY_AA=0.015, devY_AB=0.061, devY_BB=0.098, meanR_AA=1.016, meanR_AB=1.151, meanR_BB=0.92, meanTHETA_AA=0.036, meanTHETA_AB=0.5, meanTHETA_BB=0.97, meanX_AA=0.962, meanX_AB=0.575, meanX_BB=0.041, meanY_AA=0.054, meanY_AB=0.576, meanY_BB=0.878, refSNP=rs1170672, zthresh_X=0.191295862566, zthresh_Y=0.153061435119} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.899, LRR=0.047, NORMX=1.001, NORMY=0.046, R=1.048, THETA=0.029, X=17415, Y=341}]] filters=
18:11:49.351 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968848 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.884, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968848, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TATTTAGATGGACTTTTCACCAAGCTCTGAACTGGGATTTCATTTTGTTG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.099, devX_AB=0.052, devX_BB=0.015, devY_AA=0.022, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.662, meanR_AB=0.79, meanR_BB=0.676, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.638, meanX_AB=0.399, meanX_BB=0.037, meanY_AA=0.024, meanY_AB=0.391, meanY_BB=0.639, refSNP=rs113011029, zthresh_X=0.138051204865, zthresh_Y=0.165472197716} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.988, GTA=0/0, GTZ=0/0, IGC=0.486, LRR=0.095, NORMX=0.051, NORMY=0.674, R=0.725, THETA=0.952, X=1106, Y=3811}]] filters=
18:11:49.351 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
18:11:49.351 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:11:49.351 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:11:49.351 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.354 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:49.355 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:11:49.423 INFO  Funcotator - ------------------------------------------------------------
18:11:49.423 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.423 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.423 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.423 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.423 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.423 INFO  Funcotator - ------------------------------------------------------------
18:11:49.423 INFO  Funcotator - ------------------------------------------------------------
18:11:49.423 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.423 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.423 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.423 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.423 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.423 INFO  Funcotator - Inflater: IntelInflater
18:11:49.423 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.423 INFO  Funcotator - Requester pays: disabled
18:11:49.423 INFO  Funcotator - Initializing engine
18:11:49.424 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:11:49.425 INFO  Funcotator - Done initializing engine
18:11:49.425 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.425 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.425 INFO  Funcotator - Initializing data sources...
18:11:49.425 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.425 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.426 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.426 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.426 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.426 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.426 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.426 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.426 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.427 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.427 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.427 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.427 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.428 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.429 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.430 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.430 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.430 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.430 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11882644910748801061.vcf
18:11:49.433 INFO  ProgressMeter - Starting traversal
18:11:49.433 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.446 INFO  ProgressMeter -             unmapped              0.0                    21          96923.1
18:11:49.446 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:11:49.446 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:11:49.449 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.449 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11882644910748801061.vcf
18:11:49.517 INFO  Funcotator - ------------------------------------------------------------
18:11:49.517 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.517 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.517 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.517 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.517 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.517 INFO  Funcotator - ------------------------------------------------------------
18:11:49.517 INFO  Funcotator - ------------------------------------------------------------
18:11:49.517 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.517 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.517 INFO  Funcotator - Inflater: IntelInflater
18:11:49.517 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.517 INFO  Funcotator - Requester pays: disabled
18:11:49.517 INFO  Funcotator - Initializing engine
18:11:49.518 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_3_miss_clinvar_alt_only.vcf
18:11:49.518 INFO  Funcotator - Done initializing engine
18:11:49.518 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.518 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.518 INFO  Funcotator - Initializing data sources...
18:11:49.518 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.519 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.519 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.519 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.520 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.520 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.520 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.520 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.521 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.521 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.522 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.523 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.523 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.523 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.523 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.523 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10400014064039177256.vcf
18:11:49.524 INFO  ProgressMeter - Starting traversal
18:11:49.524 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.528 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
18:11:49.528 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
18:11:49.528 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:11:49.530 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.531 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out10400014064039177256.vcf
18:11:49.599 INFO  Funcotator - ------------------------------------------------------------
18:11:49.599 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.599 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.599 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.599 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.599 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.599 INFO  Funcotator - ------------------------------------------------------------
18:11:49.599 INFO  Funcotator - ------------------------------------------------------------
18:11:49.599 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.599 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.599 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.599 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.599 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.599 INFO  Funcotator - Inflater: IntelInflater
18:11:49.599 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.599 INFO  Funcotator - Requester pays: disabled
18:11:49.599 INFO  Funcotator - Initializing engine
18:11:49.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
18:11:49.601 INFO  Funcotator - Done initializing engine
18:11:49.601 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.601 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.601 INFO  Funcotator - Initializing data sources...
18:11:49.601 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.601 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.601 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.601 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.601 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.601 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.601 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.601 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.602 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.602 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.602 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.602 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.603 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.603 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.604 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.605 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.605 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.605 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.605 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.605 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13791308259278581892.vcf
18:11:49.606 INFO  ProgressMeter - Starting traversal
18:11:49.606 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.613 INFO  ProgressMeter -             unmapped              0.0                    15         128571.4
18:11:49.613 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
18:11:49.613 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
18:11:49.616 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.682 INFO  Funcotator - ------------------------------------------------------------
18:11:49.682 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.682 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.682 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.682 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.682 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.682 INFO  Funcotator - ------------------------------------------------------------
18:11:49.682 INFO  Funcotator - ------------------------------------------------------------
18:11:49.682 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.682 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.682 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.682 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.682 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.682 INFO  Funcotator - Inflater: IntelInflater
18:11:49.682 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.682 INFO  Funcotator - Requester pays: disabled
18:11:49.682 INFO  Funcotator - Initializing engine
18:11:49.683 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
18:11:49.683 INFO  Funcotator - Done initializing engine
18:11:49.683 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.683 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.683 INFO  Funcotator - Initializing data sources...
18:11:49.683 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.683 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.684 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.684 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.684 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.684 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.684 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.684 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.685 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.685 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.685 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.685 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.686 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.687 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.688 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.689 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.689 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.689 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.689 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.689 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4213939089462441066.maf
18:11:49.689 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:49.690 INFO  ProgressMeter - Starting traversal
18:11:49.690 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
18:11:49.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.695 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
18:11:49.695 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
18:11:49.695 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.695 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
18:11:49.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
18:11:49.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
18:11:49.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178943785 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
18:11:49.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178947158 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
18:11:49.698 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178952085 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
18:11:49.698 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
18:11:49.698 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
18:11:49.698 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
18:11:49.698 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.698 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13791308259278581892.vcf
18:11:49.765 INFO  Funcotator - ------------------------------------------------------------
18:11:49.765 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.765 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.765 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.765 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.765 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.765 INFO  Funcotator - ------------------------------------------------------------
18:11:49.765 INFO  Funcotator - ------------------------------------------------------------
18:11:49.765 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.765 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.765 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.765 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.765 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.765 INFO  Funcotator - Inflater: IntelInflater
18:11:49.765 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.765 INFO  Funcotator - Requester pays: disabled
18:11:49.765 INFO  Funcotator - Initializing engine
18:11:49.766 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
18:11:49.766 INFO  Funcotator - Done initializing engine
18:11:49.766 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.766 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.766 INFO  Funcotator - Initializing data sources...
18:11:49.766 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.766 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.767 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.767 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.768 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.768 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.768 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.768 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.769 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.770 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.771 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.771 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.771 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.771 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.771 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10657342009877672540.vcf
18:11:49.772 INFO  ProgressMeter - Starting traversal
18:11:49.772 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.801 INFO  ProgressMeter -             unmapped              0.0                    57         117931.0
18:11:49.801 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
18:11:49.801 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:49.803 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.869 INFO  Funcotator - ------------------------------------------------------------
18:11:49.869 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.869 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.869 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.869 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.869 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.869 INFO  Funcotator - ------------------------------------------------------------
18:11:49.869 INFO  Funcotator - ------------------------------------------------------------
18:11:49.869 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.869 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.869 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.869 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.869 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.869 INFO  Funcotator - Inflater: IntelInflater
18:11:49.869 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.869 INFO  Funcotator - Requester pays: disabled
18:11:49.869 INFO  Funcotator - Initializing engine
18:11:49.870 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
18:11:49.871 INFO  Funcotator - Done initializing engine
18:11:49.871 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.871 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.871 INFO  Funcotator - Initializing data sources...
18:11:49.871 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:11:49.871 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.871 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.871 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:49.872 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:11:49.872 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:11:49.872 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.872 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:11:49.873 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.873 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.875 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:11:49.875 INFO  Funcotator - Initializing Funcotator Engine...
18:11:49.875 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:11:49.875 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:11:49.875 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:49.875 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out2181703399023307167.maf
18:11:49.875 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:11:49.876 INFO  ProgressMeter - Starting traversal
18:11:49.876 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:11:49.878 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
18:11:49.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
18:11:49.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
18:11:49.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
18:11:49.880 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
18:11:49.881 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
18:11:49.881 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
18:11:49.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
18:11:49.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
18:11:49.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
18:11:49.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
18:11:49.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
18:11:49.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
18:11:49.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
18:11:49.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
18:11:49.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
18:11:49.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
18:11:49.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
18:11:49.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
18:11:49.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
18:11:49.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
18:11:49.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
18:11:49.890 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
18:11:49.890 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
18:11:49.890 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
18:11:49.892 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
18:11:49.892 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
18:11:49.893 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
18:11:49.893 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
18:11:49.894 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
18:11:49.894 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
18:11:49.895 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
18:11:49.896 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
18:11:49.896 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
18:11:49.896 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
18:11:49.898 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
18:11:49.898 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
18:11:49.899 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
18:11:49.899 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
18:11:49.900 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
18:11:49.900 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
18:11:49.901 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
18:11:49.902 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
18:11:49.902 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
18:11:49.902 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
18:11:49.904 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
18:11:49.904 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
18:11:49.904 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
18:11:49.905 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
18:11:49.906 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
18:11:49.906 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
18:11:49.907 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
18:11:49.907 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
18:11:49.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
18:11:49.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
18:11:49.909 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
18:11:49.909 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
18:11:49.909 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
18:11:49.909 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
18:11:49.909 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:11:49.909 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:11:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:11:49.910 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out10657342009877672540.vcf
18:11:49.983 INFO  Funcotator - ------------------------------------------------------------
18:11:49.983 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:11:49.983 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:11:49.983 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:11:49.983 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:11:49.983 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:11:49 PM UTC
18:11:49.983 INFO  Funcotator - ------------------------------------------------------------
18:11:49.983 INFO  Funcotator - ------------------------------------------------------------
18:11:49.983 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:11:49.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:11:49.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:11:49.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:11:49.983 INFO  Funcotator - Deflater: IntelDeflater
18:11:49.983 INFO  Funcotator - Inflater: IntelInflater
18:11:49.983 INFO  Funcotator - GCS max retries/reopens: 20
18:11:49.983 INFO  Funcotator - Requester pays: disabled
18:11:49.983 INFO  Funcotator - Initializing engine
18:11:49.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
18:11:49.985 INFO  Funcotator - Done initializing engine
18:11:49.985 INFO  Funcotator - Skipping sequence dictionary validation.
18:11:49.985 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:11:49.985 INFO  Funcotator - Initializing data sources...
18:11:49.985 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:11:49.985 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:11:49.985 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:49.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:49.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:49.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:49.988 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:11:49.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:11:49.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:11:50.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:11:50.049 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:11:50.057 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:11:50.057 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:11:50.057 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:11:50.058 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:11:50.636 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:11:50.710 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:50.710 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:11:50.711 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:11:50.711 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:11:50.793 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:11:50.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:50.793 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:11:50.820 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:11:50.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:11:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:11:50.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:11:50.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:11:50.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:50.822 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:11:50.822 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:50.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:50.827 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:11:50.829 INFO  Funcotator - Initializing Funcotator Engine...
18:11:50.829 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:11:50.829 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:11:50.829 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6887862548920490007.vcf
18:11:50.830 INFO  ProgressMeter - Starting traversal
18:11:50.830 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:07.751 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7091.8
18:12:08.263 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
18:12:08.264 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
18:12:09.082 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           6762.0
18:12:09.082 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
18:12:09.082 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
18:12:09.083 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.32 minutes.
Runtime.totalMemory()=3045064704
18:12:09.151 INFO  Funcotator - ------------------------------------------------------------
18:12:09.151 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:09.151 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:09.151 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:09.151 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:09.151 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:09 PM UTC
18:12:09.151 INFO  Funcotator - ------------------------------------------------------------
18:12:09.151 INFO  Funcotator - ------------------------------------------------------------
18:12:09.151 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:09.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:09.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:09.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:09.151 INFO  Funcotator - Deflater: IntelDeflater
18:12:09.151 INFO  Funcotator - Inflater: IntelInflater
18:12:09.151 INFO  Funcotator - GCS max retries/reopens: 20
18:12:09.151 INFO  Funcotator - Requester pays: disabled
18:12:09.151 INFO  Funcotator - Initializing engine
18:12:09.152 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
18:12:09.153 INFO  Funcotator - Done initializing engine
18:12:09.153 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:09.153 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:09.153 INFO  Funcotator - Initializing data sources...
18:12:09.153 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
18:12:09.153 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:09.153 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:12:09.153 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:12:09.153 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:12:09.154 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:12:09.155 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:09.155 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
18:12:09.156 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
18:12:09.226 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
18:12:09.245 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
18:12:09.252 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:12:09.253 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
18:12:09.253 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
18:12:09.253 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
18:12:09.840 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
18:12:09.879 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:12:09.879 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:09.879 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
18:12:09.880 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
18:12:09.984 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:12:09.984 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:12:09.985 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
18:12:10.012 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
18:12:10.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:12:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:12:10.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
18:12:10.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:12:10.014 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:12:10.014 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
18:12:10.015 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:12:10.017 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:12:10.019 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
18:12:10.021 INFO  Funcotator - Initializing Funcotator Engine...
18:12:10.021 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:12:10.021 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:12:10.021 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1990398869989758036.maf
18:12:10.022 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:12:10.022 INFO  ProgressMeter - Starting traversal
18:12:10.022 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:26.666 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7209.8
18:12:27.184 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
18:12:27.185 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
18:12:28.016 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           6859.0
18:12:28.016 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
18:12:28.016 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
18:12:28.017 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.31 minutes.
Runtime.totalMemory()=3045064704
18:12:28.018 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6887862548920490007.vcf
18:12:28.384 INFO  Funcotator - ------------------------------------------------------------
18:12:28.384 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:28.384 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:28.384 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:28.384 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:28.384 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:28 PM UTC
18:12:28.384 INFO  Funcotator - ------------------------------------------------------------
18:12:28.384 INFO  Funcotator - ------------------------------------------------------------
18:12:28.384 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:28.384 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:28.384 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:28.384 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:28.384 INFO  Funcotator - Deflater: IntelDeflater
18:12:28.384 INFO  Funcotator - Inflater: IntelInflater
18:12:28.384 INFO  Funcotator - GCS max retries/reopens: 20
18:12:28.384 INFO  Funcotator - Requester pays: disabled
18:12:28.384 INFO  Funcotator - Initializing engine
18:12:28.385 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:12:28.400 INFO  Funcotator - Done initializing engine
18:12:28.400 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:28.400 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:28.400 INFO  Funcotator - Initializing data sources...
18:12:28.400 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:12:28.400 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:28.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:12:28.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.400 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:28.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.400 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:28.401 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:12:28.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.402 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:12:28.402 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.418 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.425 INFO  Funcotator - Initializing Funcotator Engine...
18:12:28.432 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:12:28.432 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out169918910692774363.vcf
18:12:28.444 INFO  ProgressMeter - Starting traversal
18:12:28.444 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:28.467 INFO  ProgressMeter -             unmapped              0.0                   100         260869.6
18:12:28.467 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
18:12:28.467 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:12:28.473 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:28.537 INFO  Funcotator - ------------------------------------------------------------
18:12:28.537 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:28.537 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:28.537 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:28.537 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:28.537 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:28 PM UTC
18:12:28.537 INFO  Funcotator - ------------------------------------------------------------
18:12:28.537 INFO  Funcotator - ------------------------------------------------------------
18:12:28.537 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:28.537 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:28.537 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:28.537 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:28.537 INFO  Funcotator - Deflater: IntelDeflater
18:12:28.537 INFO  Funcotator - Inflater: IntelInflater
18:12:28.537 INFO  Funcotator - GCS max retries/reopens: 20
18:12:28.537 INFO  Funcotator - Requester pays: disabled
18:12:28.537 INFO  Funcotator - Initializing engine
18:12:28.538 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
18:12:28.553 INFO  Funcotator - Done initializing engine
18:12:28.553 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:28.553 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:28.553 INFO  Funcotator - Initializing data sources...
18:12:28.553 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:12:28.553 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:28.553 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.553 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:12:28.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.554 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:28.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.554 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:28.554 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
18:12:28.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
18:12:28.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.555 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:12:28.555 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.563 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.571 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
18:12:28.579 INFO  Funcotator - Initializing Funcotator Engine...
18:12:28.583 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
18:12:28.583 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out18235032707207478123.maf
18:12:28.584 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:12:28.584 INFO  ProgressMeter - Starting traversal
18:12:28.584 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:28.587 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179126640-179126641 Q178.26 of type=INDEL alleles=[AT*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.408, ClippingRankSum=-6.260e-01, DB=true, DP=81, ExcessHet=3.0103, FS=6.956, MLEAC=1, MLEAF=0.167, MQ=59.86, MQRankSum=1.22, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=7.13, ReadPosRankSum=-7.890e-01, SOR=2.424, VQSLOD=0.274, culprit=FS} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:23,0:23:66:.:.:0,66,769	0/0:24,0:24:23:.:.:0,23,686	0/1:13,12:25:99:0|1:179126640_AT_A:187,0,259 filters=
18:12:28.591 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179127567 Q312.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.097, ClippingRankSum=0.954, DB=true, DP=93, ExcessHet=3.0103, FS=1.440, MLEAC=1, MLEAF=0.167, MQ=54.41, MQRankSum=-3.289e+00, NEGATIVE_TRAIN_SITE=true, QD=9.76, ReadPosRankSum=0.993, SOR=0.392, VQSLOD=-1.168e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:79:0,79,1018	0/0:30,0:30:90:0,90,982	0/1:20,12:32:99:321,0,579 filters=
18:12:28.592 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179128974 Q1462.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.580, ClippingRankSum=0.348, DB=true, DP=63, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=38.22, MQRankSum=-2.159e+00, QD=23.22, ReadPosRankSum=-2.300e-02, SOR=0.823, VQSLOD=-5.665e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,17:17:51:581,51,0	1/1:0,18:18:54:600,54,0	0/1:16,12:28:99:296,0,462 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.592 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179129966 Q471.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.129e+00, ClippingRankSum=2.07, DB=true, DP=97, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=44.70, MQRankSum=-2.728e+00, QD=16.83, ReadPosRankSum=1.55, SOR=0.871, VQSLOD=-2.880e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:90:0,90,1350	0/0:38,0:38:99:0,114,1181	0/1:11,17:28:99:480,0,297 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.592 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179130674 Q425.12 of type=SNP alleles=[A*, G] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-6.110e-01, ClippingRankSum=1.19, DB=true, DP=80, ExcessHet=3.9794, FS=6.065, MLEAC=2, MLEAF=0.333, MQ=40.44, MQRankSum=-5.530e-01, QD=8.02, ReadPosRankSum=1.71, SOR=1.596, VQSLOD=-5.340e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:1|0:179130671_G_T:187,0,590	0/1:16,10:26:99:.:.:249,0,464	0/0:27,0:27:56:.:.:0,56,879 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.592 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179134890 Q30.94 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.426, ClippingRankSum=-2.840e-01, DB=true, DP=82, ExcessHet=4.7712, FS=19.638, MLEAC=1, MLEAF=0.167, MQ=59.10, MQRankSum=0.853, NEGATIVE_TRAIN_SITE=true, QD=1.29, ReadPosRankSum=-1.706e+00, SOR=3.590, VQSLOD=-4.392e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:0:0,0,686	0/0:30,0:30:0:0,0,785	0/1:19,5:24:37:37,0,445 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.593 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179135392-179135396 Q855.09 of type=INDEL alleles=[CATAT*, C, CAT, CATATAT] attr={AC=[1, 2, 2], AF=[0.167, 0.333, 0.333], AN=6, BaseQRankSum=0.591, ClippingRankSum=-1.970e-01, DB=true, DP=63, ExcessHet=3.0103, FS=0.000, MLEAC=[1, 2, 2], MLEAF=[0.167, 0.333, 0.333], MQ=59.47, MQRankSum=1.38, QD=21.38, ReadPosRankSum=-4.000e-01, SOR=0.770, VQSLOD=2.43, culprit=FS} GT=GT:AD:DP:GQ:PL	1/2:0,2,5,0:7:54:180,146,284,54,0,60,180,146,54,180	2/3:0,0,6,9:15:99:535,535,535,375,375,357,177,177,0,266	0/3:13,0,0,5:18:99:171,210,787,210,787,787,0,577,577,562 filters=
18:12:28.593 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179139036 Q2999.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-4.360e-01, ClippingRankSum=-1.497e+00, DB=true, DP=119, ExcessHet=3.0103, FS=0.876, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.470e-01, POSITIVE_TRAIN_SITE=true, QD=25.21, ReadPosRankSum=0.931, SOR=0.913, VQSLOD=16.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1077,99,0	1/1:0,42:42:99:1409,126,0	0/1:24,20:44:99:528,0,682 filters=
18:12:28.593 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179140609 Q69.99 of type=INDEL alleles=[C*, CA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.978, ClippingRankSum=-5.330e-01, DB=true, DP=66, ExcessHet=3.9794, FS=2.480, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.437, NEGATIVE_TRAIN_SITE=true, QD=5.38, ReadPosRankSum=0.533, SOR=1.981, VQSLOD=-1.111e+00, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:21,0:21:0:0,0,39	0/1:8,5:13:76:76,0,120	0/0:26,0:26:0:0,0,506 filters=
18:12:28.593 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179143781 Q477.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.21, ClippingRankSum=0.343, DB=true, DP=101, ExcessHet=3.0103, FS=8.008, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.886, POSITIVE_TRAIN_SITE=true, QD=14.46, ReadPosRankSum=0.705, SOR=0.511, VQSLOD=16.48, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,101,1267	0/0:31,0:31:90:0,90,1168	0/1:15,18:33:99:486,0,402 filters=
18:12:28.594 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179145270 Q467.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.60, ClippingRankSum=-1.870e-01, DP=94, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.040e-01, QD=15.58, ReadPosRankSum=0.644, SOR=0.941, VQSLOD=15.70, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,99,1485	0/1:14,16:30:99:476,0,330	0/0:27,0:27:81:0,81,838 filters=
18:12:28.594 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179145549 Q26.98 of type=INDEL alleles=[C*, CA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.888, ClippingRankSum=0.691, DP=58, ExcessHet=4.7712, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=58.74, MQRankSum=-1.875e+00, NEGATIVE_TRAIN_SITE=true, QD=2.08, ReadPosRankSum=-6.910e-01, SOR=0.260, VQSLOD=-5.419e-01, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:18,0:18:0:0,0,278	0/0:19,0:19:0:0,0,263	0/1:11,2:13:33:33,0,159 filters=
18:12:28.594 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179150203 Q257.25 of type=SNP alleles=[T*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.427, ClippingRankSum=-7.500e-02, DP=100, ExcessHet=3.0103, FS=1.768, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.276, QD=9.53, ReadPosRankSum=0.025, SOR=1.402, VQSLOD=15.42, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:76:0,76,1186	0/0:36,0:36:99:0,100,1272	0/1:17,10:27:99:266,0,505 filters=
18:12:28.594 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179153825-179153826 Q3030.89 of type=INDEL alleles=[TG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-4.150e-01, ClippingRankSum=0.327, DB=true, DP=114, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-5.890e-01, POSITIVE_TRAIN_SITE=true, QD=27.31, ReadPosRankSum=-6.330e-01, SOR=0.627, VQSLOD=5.19, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1013,93,0	1/1:0,51:51:99:1662,153,0	0/1:15,14:29:99:370,0,399 filters=
18:12:28.594 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179162859 Q215.29 of type=INDEL alleles=[T*, TA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.426, ClippingRankSum=0.182, DP=112, ExcessHet=3.0103, FS=1.451, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.872, QD=6.94, ReadPosRankSum=0.791, SOR=0.957, VQSLOD=0.879, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,105,1255	0/0:41,0:41:88:0,88,1285	0/1:19,12:31:99:224,0,411 filters=
18:12:28.595 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179163705 Q523.25 of type=SNP alleles=[A*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-4.440e-01, ClippingRankSum=-3.200e-02, DB=true, DP=102, ExcessHet=3.0103, FS=6.944, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.317, POSITIVE_TRAIN_SITE=true, QD=14.53, ReadPosRankSum=0.697, SOR=0.750, VQSLOD=17.08, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:90:0,90,1043	0/0:34,0:34:99:0,102,1121	0/1:17,19:36:99:532,0,471 filters=
18:12:28.595 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170066 Q304.31 of type=INDEL alleles=[A*, ACG] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.317, ClippingRankSum=-1.000e+00, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.635e+00, QD=11.27, ReadPosRankSum=0.903, SOR=0.582, VQSLOD=2.47, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:45:0,45,675	0/0:36,0:36:18:0,18,270	0/1:15,12:27:99:313,0,416 filters=
18:12:28.595 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170076 Q2160.25 of type=INDEL alleles=[G*, GCA, GCACA] attr={AC=[3, 1], AF=[0.500, 0.167], AN=6, BaseQRankSum=2.14, ClippingRankSum=1.71, DP=97, ExcessHet=3.9794, FS=2.020, MLEAC=[3, 1], MLEAF=[0.500, 0.167], MQ=60.00, MQRankSum=0.066, POSITIVE_TRAIN_SITE=true, QD=27.70, ReadPosRankSum=0.131, SOR=0.633, VQSLOD=3.22, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/1:11,11,0:22:99:429,0,498,462,531,993	1/1:0,28,0:28:93:1368,93,0,1368,93,1369	0/2:14,0,14:28:99:386,399,763,0,365,414 filters=
18:12:28.595 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179172828 Q461.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.306, ClippingRankSum=-8.830e-01, DB=true, DP=103, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.420e-01, POSITIVE_TRAIN_SITE=true, QD=13.98, ReadPosRankSum=0.342, SOR=0.582, VQSLOD=17.04, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,99,1485	0/0:36,0:36:99:0,102,1211	0/1:16,17:33:99:470,0,437 filters=
18:12:28.596 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173402 Q170.95 of type=SNP alleles=[T*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-3.260e-01, ClippingRankSum=1.23, DP=85, ExcessHet=4.7712, FS=29.768, MLEAC=1, MLEAF=0.167, MQ=59.76, MQRankSum=0.176, NEGATIVE_TRAIN_SITE=true, QD=6.33, ReadPosRankSum=-2.084e+00, SOR=4.799, VQSLOD=-9.051e+00, culprit=FS} GT=GT:AD:DP:GQ:PL	0/1:17,10:27:99:177,0,472	0/0:26,0:26:0:0,0,478	0/0:31,0:31:0:0,0,511 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.596 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173404 Q155.16 of type=MIXED alleles=[C*, A, CAA] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-8.980e-01, ClippingRankSum=0.477, DB=true, DP=71, ExcessHet=3.9794, FS=60.204, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=63.07, MQRankSum=-7.950e-01, QD=3.69, ReadPosRankSum=-1.941e+00, SOR=4.282, VQSLOD=-8.048e+00, culprit=FS} GT=GT:AD:DP:GQ:PL	0/1:8,9,0:17:99:114,0,173,138,198,336	0/0:8,0,0:10:24:0,24,153,24,153,153	0/2:19,0,6:25:58:58,114,584,0,470,451 filters=VQSRTrancheINDEL99.90to99.95
18:12:28.596 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179177312-179177313 Q580.48 of type=INDEL alleles=[CT*, C] attr={AC=4, AF=0.667, AN=6, BaseQRankSum=-4.960e-01, ClippingRankSum=0.996, DB=true, DP=96, ExcessHet=3.6798, FS=24.502, MLEAC=4, MLEAF=0.667, MQ=59.28, MQRankSum=-2.370e-01, POSITIVE_TRAIN_SITE=true, QD=9.67, ReadPosRankSum=0.992, SOR=2.238, VQSLOD=0.814, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/1:3,15:18:0:277,0,0	1/1:1,13:14:31:289,31,0	0/1:23,5:29:26:26,0,379 filters=
18:12:28.596 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179178119-179178120 Q320.25 of type=INDEL alleles=[GT*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-3.200e-02, ClippingRankSum=0.613, DB=true, DP=109, ExcessHet=3.0103, FS=1.824, MLEAC=1, MLEAF=0.167, MQ=59.26, MQRankSum=0.549, QD=13.92, ReadPosRankSum=0.032, SOR=1.473, VQSLOD=0.739, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:72:0,72,936	0/0:42,0:42:56:0,56,1260	0/1:8,15:23:99:329,0,142 filters=
18:12:28.597 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179184000-179184003 Q687.25 of type=INDEL alleles=[TAGA*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-7.160e-01, ClippingRankSum=-1.447e+00, DB=true, DP=107, ExcessHet=3.0103, FS=1.279, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.424, POSITIVE_TRAIN_SITE=true, QD=18.09, ReadPosRankSum=-1.500e-02, SOR=0.976, VQSLOD=2.98, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:78:0,78,1170	0/0:36,0:36:99:0,99,1485	0/1:20,18:38:99:696,0,964 filters=
18:12:28.597 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179187736 Q269.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.02, ClippingRankSum=-1.023e+00, DB=true, DP=58, ExcessHet=3.0103, FS=1.804, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.147e+00, POSITIVE_TRAIN_SITE=true, QD=11.71, ReadPosRankSum=0.031, SOR=1.179, VQSLOD=14.53, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:17,0:17:51:0,51,551	0/0:18,0:18:54:0,54,586	0/1:13,10:23:99:278,0,383 filters=
18:12:28.597 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190789 Q432.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.043e+00, ClippingRankSum=1.94, DB=true, DP=86, ExcessHet=3.0103, FS=10.627, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.513, POSITIVE_TRAIN_SITE=true, QD=12.35, ReadPosRankSum=1.31, SOR=1.991, VQSLOD=17.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:81:0,81,918	0/1:19,16:35:99:441,0,575	0/0:24,0:24:63:0,63,945 filters=
18:12:28.597 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190993 Q526.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.878, ClippingRankSum=-1.700e-02, DB=true, DP=91, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.160e-01, POSITIVE_TRAIN_SITE=true, QD=15.04, ReadPosRankSum=0.248, SOR=0.727, VQSLOD=17.12, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:63:0,63,769	0/0:34,0:34:99:0,102,1142	0/1:16,19:35:99:535,0,431 filters=
18:12:28.597 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179192974 Q4132.69 of type=SNP alleles=[C*, T] attr={AC=6, AF=1.00, AN=6, DB=true, DP=118, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=30.55, SOR=0.781, VQSLOD=20.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1203,99,0	1/1:0,47:47:99:1701,141,0	1/1:0,37:37:99:1242,111,0 filters=
18:12:28.598 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179201626 Q30.26 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-6.480e-01, ClippingRankSum=0.034, DP=80, ExcessHet=3.0103, FS=5.787, MLEAC=1, MLEAF=0.167, MQ=59.33, MQRankSum=0.785, NEGATIVE_TRAIN_SITE=true, QD=1.12, ReadPosRankSum=0.102, SOR=2.799, VQSLOD=-2.303e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:32:0,32,729	0/0:24,0:24:43:0,43,685	0/1:23,4:27:39:39,0,624 filters=VQSRTrancheSNP99.90to100.00
18:12:28.598 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179204486 Q390.25 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.59, ClippingRankSum=-5.460e-01, DB=true, DP=103, ExcessHet=3.0103, FS=1.485, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.768e+00, POSITIVE_TRAIN_SITE=true, QD=13.46, ReadPosRankSum=-1.960e-01, SOR=0.400, VQSLOD=16.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1222	0/0:36,0:36:99:0,99,1340	0/1:15,14:29:99:399,0,384 filters=
18:12:28.598 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179205020-179205028 Q89.08 of type=INDEL alleles=[CAAAAAAAA*, C] attr={AC=1, AF=0.250, AN=4, BaseQRankSum=-8.500e-01, ClippingRankSum=0.250, DP=62, ExcessHet=3.9794, FS=2.350, MLEAC=1, MLEAF=0.250, MQ=44.00, MQRankSum=0.050, NEGATIVE_TRAIN_SITE=true, QD=4.69, ReadPosRankSum=0.633, SOR=1.567, VQSLOD=-1.131e+00, culprit=QD} GT=GT:AD:DP:GQ:PL	./.:17,0:17:.:0,0,0	0/1:15,4:19:95:95,0,871	0/0:20,0:20:0:0,0,417 filters=
18:12:28.598 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179206086-179206087 Q139.56 of type=INDEL alleles=[CT*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.204, ClippingRankSum=-1.220e-01, DP=93, ExcessHet=3.0103, FS=1.829, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-4.100e-02, POSITIVE_TRAIN_SITE=true, QD=7.35, ReadPosRankSum=-6.940e-01, SOR=0.976, VQSLOD=2.37, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:96:0,96,1440	0/0:30,0:30:6:0,6,814	0/1:9,10:19:91:148,0,91 filters=
18:12:28.599 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207079 Q2308.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.93, ClippingRankSum=0.350, DB=true, DP=91, ExcessHet=3.0103, FS=1.015, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.590e-01, POSITIVE_TRAIN_SITE=true, QD=25.65, ReadPosRankSum=0.411, SOR=0.479, VQSLOD=17.10, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:1,22:23:34:728,34,0	1/1:0,30:30:90:1020,90,0	0/1:17,20:37:99:575,0,460 filters=
18:12:28.599 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207762 Q438.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.38, ClippingRankSum=-9.390e-01, DB=true, DP=105, ExcessHet=3.0103, FS=3.069, MLEAC=1, MLEAF=0.167, MQ=59.78, MQRankSum=0.143, POSITIVE_TRAIN_SITE=true, QD=12.17, ReadPosRankSum=1.03, SOR=0.293, VQSLOD=1.85, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,102,1257	0/0:33,0:33:99:0,99,1127	0/1:20,16:36:99:447,0,527 filters=
18:12:28.599 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215394 Q561.25 of type=SNP alleles=[T*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.081, ClippingRankSum=0.813, DB=true, DP=110, ExcessHet=3.0103, FS=7.302, MLEAC=1, MLEAF=0.167, MQ=58.66, MQRankSum=2.14, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=14.03, ReadPosRankSum=2.46, SOR=0.153, VQSLOD=-9.316e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:29,0:29:81:0,81,1008	0/0:41,0:41:99:0,104,1345	0/1:19,21:40:99:570,0,525 filters=
18:12:28.599 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215575 Q446.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.695, ClippingRankSum=-1.566e+00, DB=true, DP=109, ExcessHet=3.0103, FS=4.093, MLEAC=1, MLEAF=0.167, MQ=55.45, MQRankSum=-5.506e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=9.11, ReadPosRankSum=-3.940e-01, SOR=0.711, VQSLOD=-2.243e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:75:0,75,1125	0/0:32,0:32:90:0,90,1092	0/1:31,18:49:99:455,0,917 filters=
18:12:28.599 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179217522 Q469.25 of type=SNP alleles=[T*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.237, ClippingRankSum=-2.900e-01, DB=true, DP=91, ExcessHet=3.0103, FS=13.704, MLEAC=1, MLEAF=0.167, MQ=56.10, MQRankSum=-2.767e+00, NEGATIVE_TRAIN_SITE=true, QD=18.05, ReadPosRankSum=1.98, SOR=1.947, VQSLOD=-1.277e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:81:0,81,963	0/0:36,0:36:99:0,99,1242	0/1:10,16:26:99:478,0,267 filters=
18:12:28.600 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221303 Q563.25 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.100e-01, ClippingRankSum=1.65, DB=true, DP=117, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=59.98, MQRankSum=0.640, POSITIVE_TRAIN_SITE=true, QD=12.24, ReadPosRankSum=-6.400e-01, SOR=0.719, VQSLOD=3.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:33,0:33:99:0,99,1137	0/0:38,0:38:99:0,103,1236	0/1:25,21:46:99:572,0,731 filters=
18:12:28.600 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221696 Q186.62 of type=INDEL alleles=[C*, CT] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-1.580e-01, ClippingRankSum=1.42, DP=90, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=55.26, MQRankSum=-1.580e-01, QD=16.97, ReadPosRankSum=0.474, SOR=0.399, VQSLOD=2.59, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:7:0,7,730	0/0:32,0:32:26:0,26,912	1/1:1,10:11:22:203,22,0 filters=
18:12:28.600 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179224643 Q334.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.002e+00, ClippingRankSum=-1.038e+00, DB=true, DP=93, ExcessHet=3.0103, FS=1.410, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.100e-01, POSITIVE_TRAIN_SITE=true, QD=10.13, ReadPosRankSum=0.637, SOR=1.193, VQSLOD=16.65, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:63:0,63,945	0/0:36,0:36:99:0,99,1267	0/1:19,14:33:99:343,0,552 filters=
18:12:28.600 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179226199 Q4465.73 of type=INDEL alleles=[T*, TACTTG] attr={AC=6, AF=1.00, AN=6, DB=true, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=32.58, SOR=0.870, VQSLOD=4.17, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,26:26:84:1244,84,0	1/1:0,37:37:99:1684,117,0	1/1:0,33:33:99:1551,105,0 filters=
18:12:28.601 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179231630 Q153.90 of type=INDEL alleles=[C*, CT] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-9.670e-01, ClippingRankSum=1.18, DP=78, ExcessHet=0.4576, FS=7.782, MLEAC=1, MLEAF=0.167, MQ=55.92, MQRankSum=-1.182e+00, NEGATIVE_TRAIN_SITE=true, QD=12.83, ReadPosRankSum=0.107, SOR=4.804, VQSLOD=-2.689e+00, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:31:0,31,634	0/0:37,0:37:76:0,76,1115	1/1:2,10:12:3:165,3,0 filters=
18:12:28.601 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232352 Q328.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.247e+00, ClippingRankSum=0.488, DB=true, DP=106, ExcessHet=3.0103, FS=5.188, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.284e+00, POSITIVE_TRAIN_SITE=true, QD=9.95, ReadPosRankSum=0.127, SOR=0.910, VQSLOD=16.22, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1291	0/1:18,15:33:99:337,0,547	0/0:37,0:37:99:0,103,1237 filters=
18:12:28.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232509 Q343.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-8.060e-01, ClippingRankSum=-7.700e-02, DB=true, DP=104, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.957e+00, POSITIVE_TRAIN_SITE=true, QD=10.73, ReadPosRankSum=-7.670e-01, SOR=0.818, VQSLOD=16.67, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,102,1227	0/0:35,0:35:99:0,101,1177	0/1:19,13:32:99:352,0,540 filters=
18:12:28.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179236244-179236250 Q753.25 of type=INDEL alleles=[TATTGCC*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.77, ClippingRankSum=0.139, DB=true, DP=101, ExcessHet=3.0103, FS=4.716, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.670e-01, POSITIVE_TRAIN_SITE=true, QD=17.93, ReadPosRankSum=0.419, SOR=1.532, VQSLOD=1.73, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:24,0:24:69:0,69,1035	0/0:35,0:35:99:0,99,1485	0/1:22,20:42:99:762,0,1723 filters=
18:12:28.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179242400-179242401 Q224.25 of type=INDEL alleles=[GA*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=2.17, ClippingRankSum=0.952, DB=true, DP=93, ExcessHet=3.0103, FS=1.574, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.244e+00, QD=8.31, ReadPosRankSum=2.03, SOR=1.270, VQSLOD=-1.078e-01, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:55:0,55,903	0/0:32,0:32:90:0,90,1350	0/1:15,12:27:99:233,0,310 filters=
18:12:28.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179243192 Q478.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.15, ClippingRankSum=-8.050e-01, DB=true, DP=65, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=35.48, MQRankSum=0.595, POSITIVE_TRAIN_SITE=true, QD=20.79, ReadPosRankSum=-5.250e-01, SOR=1.061, VQSLOD=-7.350e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,680	0/0:21,0:21:60:0,60,900	0/1:6,17:23:99:487,0,133 filters=VQSRTrancheSNP99.90to100.00+
18:12:28.602 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244582 Q498.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.270e-01, ClippingRankSum=1.17, DB=true, DP=92, ExcessHet=3.0103, FS=19.592, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.330e-01, POSITIVE_TRAIN_SITE=true, QD=15.10, ReadPosRankSum=0.524, SOR=0.831, VQSLOD=17.78, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:78:0,78,1170	0/0:31,0:31:90:0,90,1017	0/1:15,18:33:99:507,0,377 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244703 Q365.29 of type=INDEL alleles=[G*, GA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-8.890e-01, ClippingRankSum=1.68, DB=true, DP=86, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-2.170e-01, QD=11.78, ReadPosRankSum=0.138, SOR=0.582, VQSLOD=3.58, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:19,0:19:54:0,54,810	0/0:32,0:32:71:0,71,1003	0/1:15,16:31:99:374,0,299 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179246281 Q488.25 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.206, ClippingRankSum=0.997, DB=true, DP=98, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-2.060e-01, POSITIVE_TRAIN_SITE=true, QD=13.56, ReadPosRankSum=-3.320e-01, SOR=0.914, VQSLOD=16.84, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:26,0:26:72:0,72,1080	0/0:35,0:35:99:0,105,1216	0/1:18,18:36:99:497,0,477 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179247445 Q219.25 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.988, ClippingRankSum=-3.040e-01, DB=true, DP=67, ExcessHet=3.0103, FS=7.574, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.040e-01, POSITIVE_TRAIN_SITE=true, QD=10.96, ReadPosRankSum=-7.600e-02, SOR=1.182, VQSLOD=15.60, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:19,0:19:51:0,51,765	0/0:27,0:27:72:0,72,1080	0/1:11,9:20:99:228,0,293 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249007 Q176.29 of type=INDEL alleles=[C*, CT] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.398, ClippingRankSum=-1.810e-01, DP=93, ExcessHet=3.0103, FS=14.970, MLEAC=1, MLEAF=0.167, MQ=59.54, MQRankSum=1.27, NEGATIVE_TRAIN_SITE=true, QD=8.39, ReadPosRankSum=-3.078e+00, SOR=2.047, VQSLOD=-1.813e+00, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:41:0,41,664	0/0:35,0:35:55:0,55,1006	0/1:8,13:21:92:185,0,92 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249792 Q281.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.217e+00, ClippingRankSum=0.116, DB=true, DP=94, ExcessHet=3.0103, FS=1.660, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.370e-01, POSITIVE_TRAIN_SITE=true, QD=11.72, ReadPosRankSum=-1.680e+00, SOR=0.591, VQSLOD=16.74, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,111,1246	0/0:32,0:32:81:0,81,1215	0/1:13,11:24:99:290,0,380 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249918 Q476.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=2.23, ClippingRankSum=-6.440e-01, DB=true, DP=82, ExcessHet=3.0103, FS=3.012, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-9.080e-01, POSITIVE_TRAIN_SITE=true, QD=13.61, ReadPosRankSum=1.80, SOR=1.371, VQSLOD=16.16, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:23,0:23:63:0,63,945	0/0:24,0:24:72:0,72,764	0/1:18,17:35:99:485,0,466 filters=
18:12:28.603 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250038 Q3005.69 of type=SNP alleles=[C*, T] attr={AC=6, AF=1.00, AN=6, DB=true, DP=92, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=33.77, SOR=0.809, VQSLOD=21.51, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1078,93,0	1/1:0,27:27:81:919,81,0	1/1:0,31:31:93:1022,93,0 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250846 Q392.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.082, ClippingRankSum=-5.200e-01, DB=true, DP=97, ExcessHet=3.0103, FS=3.831, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.137, POSITIVE_TRAIN_SITE=true, QD=15.69, ReadPosRankSum=-2.700e-02, SOR=0.180, VQSLOD=17.01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:81:0,81,1215	0/0:41,0:41:99:0,105,1406	0/1:11,14:25:99:401,0,307 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250872 Q279.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.094, ClippingRankSum=0.329, DB=true, DP=97, ExcessHet=3.0103, FS=6.451, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.282, POSITIVE_TRAIN_SITE=true, QD=9.97, ReadPosRankSum=0.376, SOR=2.303, VQSLOD=18.22, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:93:0,93,1153	0/0:36,0:36:99:0,102,1475	0/1:17,11:28:99:288,0,497 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251319 Q1399.10 of type=SNP alleles=[G*, A] attr={AC=2, AF=0.333, AN=6, DB=true, DP=105, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=33.31, SOR=0.693, VQSLOD=22.21, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:90:0,90,1082	0/0:30,0:30:81:0,81,1215	1/1:0,42:42:99:1416,126,0 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251568-179251569 Q272.25 of type=INDEL alleles=[GC*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.317, ClippingRankSum=-4.010e-01, DB=true, DP=88, ExcessHet=3.0103, FS=1.523, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.900e-01, POSITIVE_TRAIN_SITE=true, QD=8.78, ReadPosRankSum=-1.078e+00, SOR=1.030, VQSLOD=2.16, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:29,0:29:81:0,81,1215	0/0:27,0:27:81:0,81,878	0/1:21,10:31:99:281,0,691 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251754 Q1075.10 of type=SNP alleles=[A*, G] attr={AC=2, AF=0.333, AN=6, DB=true, DP=103, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=59.49, POSITIVE_TRAIN_SITE=true, QD=32.58, SOR=1.022, VQSLOD=4.57, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:90:0,90,1350	0/0:38,0:38:99:0,108,1620	1/1:0,33:33:99:1092,99,0 filters=
18:12:28.604 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251923 Q474.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.02, ClippingRankSum=0.707, DB=true, DP=102, ExcessHet=3.0103, FS=7.891, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.570e+00, POSITIVE_TRAIN_SITE=true, QD=13.95, ReadPosRankSum=-9.830e-01, SOR=1.806, VQSLOD=16.71, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:33,0:33:99:0,99,1107	0/0:35,0:35:99:0,99,1211	0/1:16,18:34:99:483,0,433 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251953 Q461.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-2.640e-01, ClippingRankSum=-6.420e-01, DB=true, DP=101, ExcessHet=3.0103, FS=8.162, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=1.21, POSITIVE_TRAIN_SITE=true, QD=14.41, ReadPosRankSum=1.25, SOR=1.646, VQSLOD=16.99, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,102,1152	0/0:35,0:35:99:0,99,1211	0/1:15,17:32:99:470,0,425 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179252222 Q2788.69 of type=SNP alleles=[A*, G] attr={AC=6, AF=1.00, AN=6, DB=true, DP=89, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=32.43, SOR=1.005, VQSLOD=21.87, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,20:20:59:635,59,0	1/1:0,31:31:93:1007,93,0	1/1:0,35:35:99:1160,105,0 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253641 Q2275.89 of type=SNP alleles=[C*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.56, ClippingRankSum=0.971, DB=true, DP=86, ExcessHet=3.0103, FS=10.506, MLEAC=5, MLEAF=0.833, MQ=59.96, MQRankSum=-2.430e-01, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=26.78, ReadPosRankSum=0.451, SOR=0.353, VQSLOD=0.342, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,19:19:57:630,57,0	1/1:0,32:32:96:1122,96,0	0/1:15,19:34:99:538,0,399 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253762 Q2586.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.720e-01, ClippingRankSum=-1.338e+00, DB=true, DP=114, ExcessHet=3.0103, FS=1.962, MLEAC=5, MLEAF=0.833, MQ=59.77, MQRankSum=-5.780e-01, POSITIVE_TRAIN_SITE=true, QD=24.18, ReadPosRankSum=0.352, SOR=0.768, VQSLOD=1.82, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,22:22:66:689,66,0	1/1:0,46:46:99:1468,137,0	0/1:21,18:39:99:444,0,603 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255161 Q3392.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.013e+00, ClippingRankSum=-1.013e+00, DB=true, DP=98, ExcessHet=3.0103, FS=6.010, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=0.184, QD=30.63, ReadPosRankSum=1.38, SOR=0.243, VQSLOD=1.03, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:179255161_T_G:1412,99,0	1/1:0,34:34:99:1|1:179255161_T_G:1451,102,0	0/1:13,15:28:99:0|1:179255161_T_G:544,0,490 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255164 Q3782.93 of type=INDEL alleles=[C*, CA] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.380e-01, ClippingRankSum=0.369, DB=true, DP=95, ExcessHet=3.0103, FS=2.545, MLEAC=5, MLEAF=0.833, MQ=59.82, MQRankSum=0.737, QD=28.90, ReadPosRankSum=0.921, SOR=0.383, VQSLOD=1.64, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,29:29:99:1|1:179255161_T_G:1513,105,0	1/1:0,35:35:99:1|1:179255161_T_G:1701,120,0	0/1:13,15:28:99:0|1:179255161_T_G:583,0,529 filters=
18:12:28.605 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255188 Q3232.89 of type=SNP alleles=[C*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.417, ClippingRankSum=-5.760e-01, DB=true, DP=98, ExcessHet=3.0103, FS=5.267, MLEAC=5, MLEAF=0.833, MQ=59.69, MQRankSum=-7.740e-01, POSITIVE_TRAIN_SITE=true, QD=34.76, ReadPosRankSum=0.695, SOR=0.293, VQSLOD=1.04, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,28:28:87:1|1:179255161_T_G:1264,87,0	1/1:0,34:34:99:1|1:179255161_T_G:1483,105,0	0/1:17,14:31:99:0|1:179255161_T_G:500,0,611 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255255 Q2636.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.850e-01, ClippingRankSum=0.982, DB=true, DP=102, ExcessHet=3.0103, FS=3.573, MLEAC=5, MLEAF=0.833, MQ=59.86, MQRankSum=0.032, POSITIVE_TRAIN_SITE=true, QD=26.64, ReadPosRankSum=0.095, SOR=1.109, VQSLOD=1.51, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1146,99,0	1/1:0,30:30:90:1044,90,0	0/1:19,17:36:99:461,0,551 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255327 Q2558.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.44, ClippingRankSum=1.34, DB=true, DP=106, ExcessHet=3.0103, FS=0.990, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.53, POSITIVE_TRAIN_SITE=true, QD=24.84, ReadPosRankSum=1.63, SOR=0.540, VQSLOD=16.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:98:1067,98,0	1/1:1,34:35:94:1062,94,0	0/1:17,18:35:99:444,0,476 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255934 Q3076.89 of type=SNP alleles=[A*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.408e+00, ClippingRankSum=0.974, DB=true, DP=111, ExcessHet=3.0103, FS=5.748, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-9.430e-01, POSITIVE_TRAIN_SITE=true, QD=28.23, ReadPosRankSum=1.72, SOR=0.391, VQSLOD=16.36, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1123,96,0	1/1:0,40:40:99:1355,120,0	0/1:15,22:37:99:613,0,410 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256242 Q2259.89 of type=SNP alleles=[A*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-8.490e-01, ClippingRankSum=-3.150e-01, DB=true, DP=82, ExcessHet=3.0103, FS=4.103, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.315, QD=27.56, ReadPosRankSum=-1.674e+00, SOR=0.307, VQSLOD=14.94, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,19:19:57:671,57,0	1/1:0,36:36:99:1262,108,0	0/1:14,13:27:99:341,0,395 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256462 Q2630.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.160e-01, ClippingRankSum=0.546, DB=true, DP=103, ExcessHet=3.0103, FS=3.519, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.480e-01, POSITIVE_TRAIN_SITE=true, QD=26.31, ReadPosRankSum=1.80, SOR=0.335, VQSLOD=16.39, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,28:28:84:953,84,0	1/1:0,37:37:99:1241,111,0	0/1:19,16:35:99:451,0,500 filters=
18:12:28.606 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256883 Q2600.89 of type=SNP alleles=[A*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.811, ClippingRankSum=-4.060e-01, DB=true, DP=88, ExcessHet=3.0103, FS=8.554, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-1.217e+00, POSITIVE_TRAIN_SITE=true, QD=29.56, ReadPosRankSum=1.85, SOR=0.525, VQSLOD=15.87, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1316,111,0	1/1:0,27:27:81:989,81,0	0/1:13,11:24:99:310,0,370 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257051 Q2339.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.493, ClippingRankSum=0.080, DB=true, DP=94, ExcessHet=3.0103, FS=9.170, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-4.800e-02, POSITIVE_TRAIN_SITE=true, QD=25.16, ReadPosRankSum=-7.800e-01, SOR=1.446, VQSLOD=16.26, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:859,75,0	1/1:0,32:32:96:1082,96,0	0/1:20,16:36:99:413,0,567 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257184 Q2329.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.500e-02, ClippingRankSum=1.06, DB=true, DP=87, ExcessHet=3.0103, FS=2.290, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.73, POSITIVE_TRAIN_SITE=true, QD=26.78, ReadPosRankSum=0.353, SOR=0.598, VQSLOD=15.91, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,21:21:63:738,63,0	1/1:0,29:29:87:1006,87,0	0/1:16,21:37:99:600,0,445 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257620 Q2638.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.710e-01, ClippingRankSum=0.416, DB=true, DP=105, ExcessHet=3.0103, FS=3.442, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.70, POSITIVE_TRAIN_SITE=true, QD=25.37, ReadPosRankSum=-1.318e+00, SOR=0.600, VQSLOD=16.50, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:819,75,0	1/1:0,45:45:99:1484,134,0	0/1:19,15:34:99:350,0,539 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257738 Q3124.89 of type=SNP alleles=[G*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.19, ClippingRankSum=0.766, DB=true, DP=99, ExcessHet=3.0103, FS=1.985, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.50, POSITIVE_TRAIN_SITE=true, QD=31.89, ReadPosRankSum=0.00, SOR=0.897, VQSLOD=15.63, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,19:19:60:1|1:179257738_G_T:880,60,0	1/1:0,39:39:99:1|1:179257738_G_T:1669,117,0	0/1:23,17:40:99:0|1:179257738_G_T:590,0,1285 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257767 Q3199.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.19, ClippingRankSum=-3.220e-01, DB=true, DP=100, ExcessHet=3.0103, FS=2.068, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-7.200e-01, POSITIVE_TRAIN_SITE=true, QD=32.99, ReadPosRankSum=-8.430e-01, SOR=0.922, VQSLOD=15.62, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,22:22:69:1|1:179257738_G_T:994,69,0	1/1:0,38:38:99:1|1:179257738_G_T:1652,117,0	0/1:21,16:37:99:0|1:179257738_G_T:568,0,1203 filters=
18:12:28.607 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257889-179257890 Q3069.89 of type=INDEL alleles=[TG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.155, ClippingRankSum=-6.600e-02, DP=94, ExcessHet=3.0103, FS=2.196, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.952, QD=33.74, ReadPosRankSum=0.199, SOR=0.462, VQSLOD=1.53, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,21:21:63:1|1:179257889_TG_T:901,63,0	1/1:0,41:41:99:1|1:179257889_TG_T:1761,124,0	0/1:17,12:29:99:0|1:179257889_TG_T:422,0,1693 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257891-179257898 Q3063.89 of type=INDEL alleles=[TGTGTGTG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.783, ClippingRankSum=1.16, DB=true, DP=95, ExcessHet=3.0103, FS=2.220, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.275, QD=33.30, ReadPosRankSum=-2.300e-02, SOR=0.401, VQSLOD=1.59, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,21:21:63:1|1:179257889_TG_T:901,63,0	1/1:0,41:41:99:1|1:179257889_TG_T:1761,124,0	0/1:18,12:30:99:0|1:179257889_TG_T:416,0,1755 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258111 Q2662.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.39, ClippingRankSum=1.31, DB=true, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.94, MQRankSum=1.65, POSITIVE_TRAIN_SITE=true, QD=27.45, ReadPosRankSum=0.661, SOR=0.611, VQSLOD=3.65, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:844,75,0	1/1:1,40:41:99:1336,99,0	0/1:13,18:31:99:497,0,359 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258178 Q2710.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-6.520e-01, ClippingRankSum=-1.166e+00, DB=true, DP=103, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.78, MQRankSum=-5.730e-01, QD=26.58, ReadPosRankSum=2.12, SOR=0.698, VQSLOD=3.34, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1037,96,0	1/1:0,39:39:99:1280,116,0	0/1:16,15:31:99:408,0,463 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258390 Q2940.89 of type=SNP alleles=[A*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.830e-01, ClippingRankSum=0.886, DB=true, DP=106, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-3.580e-01, POSITIVE_TRAIN_SITE=true, QD=27.74, ReadPosRankSum=0.433, SOR=0.646, VQSLOD=17.14, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1079,96,0	1/1:0,42:42:99:1416,126,0	0/1:16,16:32:99:460,0,435 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258419 Q2608.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.400e-02, ClippingRankSum=0.773, DB=true, DP=101, ExcessHet=3.0103, FS=1.047, MLEAC=5, MLEAF=0.833, MQ=59.88, MQRankSum=-6.970e-01, POSITIVE_TRAIN_SITE=true, QD=26.09, ReadPosRankSum=0.320, SOR=0.552, VQSLOD=2.41, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,27:27:81:853,81,0	1/1:0,41:41:99:1330,123,0	0/1:16,16:32:99:440,0,460 filters=
18:12:28.608 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258803 Q2882.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.135, ClippingRankSum=-1.571e+00, DB=true, DP=105, ExcessHet=3.0103, FS=3.332, MLEAC=5, MLEAF=0.833, MQ=59.82, MQRankSum=2.49, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=27.46, ReadPosRankSum=2.00, SOR=0.346, VQSLOD=1.04, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1344,111,0	1/1:0,28:28:84:1023,84,0	0/1:21,19:40:99:530,0,589 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258989 Q2795.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.076, ClippingRankSum=0.717, DB=true, DP=99, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-9.820e-01, POSITIVE_TRAIN_SITE=true, QD=28.53, ReadPosRankSum=-8.690e-01, SOR=0.603, VQSLOD=3.70, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,35:35:99:1237,105,0	1/1:0,31:31:93:1108,93,0	0/1:15,17:32:99:465,0,423 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179259033 Q2966.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.86, ClippingRankSum=-1.301e+00, DB=true, DP=100, ExcessHet=3.0103, FS=1.111, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-9.810e-01, QD=29.97, ReadPosRankSum=-7.810e-01, SOR=0.621, VQSLOD=1.10, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,40:40:99:1410,120,0	1/1:0,28:28:84:1048,84,0	0/1:13,18:31:99:523,0,359 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179259323 Q3040.89 of type=SNP alleles=[G*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.900e-01, ClippingRankSum=-7.900e-02, DB=true, DP=103, ExcessHet=3.0103, FS=7.231, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-1.713e+00, POSITIVE_TRAIN_SITE=true, QD=29.81, ReadPosRankSum=0.712, SOR=0.505, VQSLOD=16.01, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,34:34:99:1147,102,0	1/1:0,42:42:99:1460,126,0	0/1:10,16:26:99:448,0,269 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260056 Q2404.89 of type=SNP alleles=[G*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.832, ClippingRankSum=1.46, DB=true, DP=89, ExcessHet=3.0103, FS=7.907, MLEAC=5, MLEAF=0.833, MQ=59.78, MQRankSum=-1.041e+00, POSITIVE_TRAIN_SITE=true, QD=27.33, ReadPosRankSum=0.902, SOR=0.561, VQSLOD=1.54, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,23:23:69:799,69,0	1/1:0,31:31:93:1097,93,0	0/1:15,19:34:99:523,0,400 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260290 Q2662.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.500, ClippingRankSum=-1.960e-01, DB=true, DP=90, ExcessHet=3.0103, FS=1.458, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-1.327e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=29.92, ReadPosRankSum=2.02, SOR=0.383, VQSLOD=1.29, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,28:28:84:943,84,0	1/1:0,29:29:87:996,87,0	0/1:8,24:32:99:738,0,182 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260540 Q3121.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.63, ClippingRankSum=0.380, DB=true, DP=108, ExcessHet=3.0103, FS=5.368, MLEAC=5, MLEAF=0.833, MQ=59.61, MQRankSum=-1.553e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=28.91, ReadPosRankSum=-1.775e+00, SOR=0.458, VQSLOD=0.718, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	1/1:0,30:30:90:1133,90,0	1/1:0,42:42:99:1450,126,0	0/1:17,19:36:99:553,0,413 filters=
18:12:28.609 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260754 Q3003.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.208, ClippingRankSum=1.56, DB=true, DP=106, ExcessHet=3.0103, FS=3.942, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.727, POSITIVE_TRAIN_SITE=true, QD=28.34, ReadPosRankSum=0.467, SOR=0.675, VQSLOD=16.45, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1275,111,0	1/1:0,43:43:99:1464,129,0	0/1:15,11:26:99:279,0,444 filters=
18:12:28.610 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260816 Q2359.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.402e+00, ClippingRankSum=-7.350e-01, DB=true, DP=91, ExcessHet=3.0103, FS=1.158, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-6.680e-01, POSITIVE_TRAIN_SITE=true, QD=25.93, ReadPosRankSum=-8.680e-01, SOR=0.750, VQSLOD=16.47, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1017,93,0	1/1:0,38:38:99:1180,112,0	0/1:13,9:22:99:177,0,376 filters=
18:12:28.617 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260901 Q2768.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.025, ClippingRankSum=0.666, DB=true, DP=97, ExcessHet=3.0103, FS=4.486, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-7.650e-01, POSITIVE_TRAIN_SITE=true, QD=28.55, ReadPosRankSum=-7.650e-01, SOR=0.464, VQSLOD=16.16, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1057,96,0	1/1:0,38:38:99:1286,114,0	0/1:11,16:27:99:440,0,272 filters=
18:12:28.617 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260930 Q2820.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-7.470e-01, ClippingRankSum=0.346, DB=true, DP=104, ExcessHet=3.0103, FS=5.049, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.26, POSITIVE_TRAIN_SITE=true, QD=27.12, ReadPosRankSum=1.55, SOR=0.800, VQSLOD=15.85, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1092,96,0	1/1:0,39:39:99:1356,117,0	0/1:19,14:33:99:387,0,551 filters=
18:12:28.618 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262286 Q517.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-4.900e-02, ClippingRankSum=-8.900e-01, DP=111, ExcessHet=3.0103, FS=3.836, MLEAC=1, MLEAF=0.167, MQ=59.93, MQRankSum=-9.380e-01, QD=8.92, ReadPosRankSum=0.210, SOR=1.276, VQSLOD=-9.570e-02, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:18,0:18:51:0,51,765	0/0:35,0:35:99:0,99,1235	0/1:37,21:58:99:526,0,1082 filters=
18:12:28.618 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262480 Q2208.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.430e-01, ClippingRankSum=-5.800e-02, DB=true, DP=95, ExcessHet=3.0103, FS=3.148, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=2.00, POSITIVE_TRAIN_SITE=true, QD=23.25, ReadPosRankSum=0.405, SOR=0.414, VQSLOD=16.20, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,21:21:63:730,63,0	1/1:0,29:29:87:1003,87,0	0/1:27,18:45:99:490,0,763 filters=
18:12:28.618 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262545 Q2541.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.79, ClippingRankSum=0.065, DB=true, DP=112, ExcessHet=3.0103, FS=3.965, MLEAC=5, MLEAF=0.833, MQ=59.93, MQRankSum=0.116, POSITIVE_TRAIN_SITE=true, QD=23.11, ReadPosRankSum=0.578, SOR=0.384, VQSLOD=1.95, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:1,29:30:80:978,80,0	1/1:0,32:32:96:1142,96,0	0/1:31,17:48:99:436,0,883 filters=
18:12:28.618 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262851 Q766.12 of type=SNP alleles=[G*, A] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=0.812, ClippingRankSum=1.18, DB=true, DP=92, ExcessHet=3.9794, FS=1.012, MLEAC=2, MLEAF=0.333, MQ=59.92, MQRankSum=-6.730e-01, POSITIVE_TRAIN_SITE=true, QD=13.44, ReadPosRankSum=1.42, SOR=0.922, VQSLOD=1.58, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:14,15:29:99:454,0,399	0/1:16,12:28:99:323,0,447	0/0:34,0:34:88:0,88,1082 filters=
18:12:28.618 INFO  ProgressMeter -             unmapped              0.0                   100         176470.6
18:12:28.618 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
18:12:28.618 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:12:28.619 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:28.619 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out169918910692774363.vcf
18:12:28.747 INFO  Funcotator - ------------------------------------------------------------
18:12:28.747 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:28.747 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:28.747 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:28.747 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:28.747 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:28 PM UTC
18:12:28.747 INFO  Funcotator - ------------------------------------------------------------
18:12:28.747 INFO  Funcotator - ------------------------------------------------------------
18:12:28.747 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:28.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:28.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:28.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:28.747 INFO  Funcotator - Deflater: IntelDeflater
18:12:28.747 INFO  Funcotator - Inflater: IntelInflater
18:12:28.747 INFO  Funcotator - GCS max retries/reopens: 20
18:12:28.747 INFO  Funcotator - Requester pays: disabled
18:12:28.747 INFO  Funcotator - Initializing engine
18:12:28.748 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
18:12:28.748 INFO  Funcotator - Done initializing engine
18:12:28.748 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:28.748 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:28.748 INFO  Funcotator - Initializing data sources...
18:12:28.748 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:12:28.749 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:28.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.749 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:28.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.749 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:28.749 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.750 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.750 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.750 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:12:28.750 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.752 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.753 INFO  Funcotator - Initializing Funcotator Engine...
18:12:28.753 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:12:28.753 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:12:28.753 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:12:28.753 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15586799621902969788.vcf
18:12:28.754 INFO  ProgressMeter - Starting traversal
18:12:28.754 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:28.782 INFO  ProgressMeter -             unmapped              0.0                    57         122142.9
18:12:28.782 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
18:12:28.782 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:12:28.785 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:28.850 INFO  Funcotator - ------------------------------------------------------------
18:12:28.850 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:28.850 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:28.850 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:28.850 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:28.850 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:28 PM UTC
18:12:28.850 INFO  Funcotator - ------------------------------------------------------------
18:12:28.850 INFO  Funcotator - ------------------------------------------------------------
18:12:28.850 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:28.850 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:28.850 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:28.850 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:28.850 INFO  Funcotator - Deflater: IntelDeflater
18:12:28.850 INFO  Funcotator - Inflater: IntelInflater
18:12:28.850 INFO  Funcotator - GCS max retries/reopens: 20
18:12:28.850 INFO  Funcotator - Requester pays: disabled
18:12:28.850 INFO  Funcotator - Initializing engine
18:12:28.851 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
18:12:28.851 INFO  Funcotator - Done initializing engine
18:12:28.851 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:28.851 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:28.851 INFO  Funcotator - Initializing data sources...
18:12:28.851 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:12:28.851 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:28.851 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.851 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.851 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.851 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:28.851 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.851 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:28.852 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.852 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.852 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.852 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:12:28.853 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.854 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.855 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.855 INFO  Funcotator - Initializing Funcotator Engine...
18:12:28.855 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:12:28.855 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:12:28.855 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
18:12:28.855 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17975730017899409378.maf
18:12:28.856 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
18:12:28.856 INFO  ProgressMeter - Starting traversal
18:12:28.856 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:28.858 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
18:12:28.858 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
18:12:28.859 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
18:12:28.859 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
18:12:28.860 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
18:12:28.860 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
18:12:28.861 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
18:12:28.862 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
18:12:28.862 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
18:12:28.862 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
18:12:28.862 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
18:12:28.863 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
18:12:28.863 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
18:12:28.864 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
18:12:28.865 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
18:12:28.865 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
18:12:28.866 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
18:12:28.866 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
18:12:28.866 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
18:12:28.867 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
18:12:28.868 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
18:12:28.868 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
18:12:28.869 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
18:12:28.870 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
18:12:28.870 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
18:12:28.871 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
18:12:28.872 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
18:12:28.873 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
18:12:28.873 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
18:12:28.873 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
18:12:28.874 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
18:12:28.875 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
18:12:28.875 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
18:12:28.876 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
18:12:28.876 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
18:12:28.877 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
18:12:28.877 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
18:12:28.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
18:12:28.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
18:12:28.879 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
18:12:28.880 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
18:12:28.881 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
18:12:28.881 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
18:12:28.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
18:12:28.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
18:12:28.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
18:12:28.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
18:12:28.884 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
18:12:28.884 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
18:12:28.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
18:12:28.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
18:12:28.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
18:12:28.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
18:12:28.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
18:12:28.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
18:12:28.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
18:12:28.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
18:12:28.889 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
18:12:28.889 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
18:12:28.889 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
18:12:28.889 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:28.890 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15586799621902969788.vcf
18:12:28.983 INFO  Funcotator - ------------------------------------------------------------
18:12:28.983 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:28.983 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:28.983 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:28.983 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:28.983 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:28 PM UTC
18:12:28.983 INFO  Funcotator - ------------------------------------------------------------
18:12:28.983 INFO  Funcotator - ------------------------------------------------------------
18:12:28.983 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:28.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:28.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:28.983 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:28.983 INFO  Funcotator - Deflater: IntelDeflater
18:12:28.983 INFO  Funcotator - Inflater: IntelInflater
18:12:28.983 INFO  Funcotator - GCS max retries/reopens: 20
18:12:28.983 INFO  Funcotator - Requester pays: disabled
18:12:28.983 INFO  Funcotator - Initializing engine
18:12:28.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
18:12:28.985 INFO  Funcotator - Done initializing engine
18:12:28.985 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:28.985 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:28.985 INFO  Funcotator - Initializing data sources...
18:12:28.985 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
18:12:28.985 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:28.985 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.985 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.986 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:28.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.986 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:28.986 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:28.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:28.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.987 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
18:12:28.987 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.988 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.989 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
18:12:28.990 INFO  Funcotator - Initializing Funcotator Engine...
18:12:28.990 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:12:28.990 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:12:28.990 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15898810793324408195.maf
18:12:28.990 INFO  ProgressMeter - Starting traversal
18:12:28.990 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:28.993 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178872355 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.823, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178872355, ILLUMINA_STRAND=TOP, N_AA=4, N_AB=194, N_BB=1053, PROBE_A=AATGTGTTACAATCTGTCCCCCACCATATACATATACAAAGTAGCAGTCC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.02, devTHETA_AB=0.035, devTHETA_BB=0.018, devX_AA=0.095, devX_AB=0.05, devX_BB=0.02, devY_AA=0.022, devY_AB=0.06, devY_BB=0.094, meanR_AA=0.748, meanR_AB=0.789, meanR_BB=0.755, meanTHETA_AA=0.052, meanTHETA_AB=0.569, meanTHETA_BB=0.946, meanX_AA=0.692, meanX_AB=0.352, meanX_BB=0.059, meanY_AA=0.056, meanY_AB=0.437, meanY_BB=0.695, refSNP=rs11706842, zthresh_X=0.18402316111, zthresh_Y=0.185250013887} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.514, GTA=1/0, GTZ=1/0, IGC=0.849, LRR=-0.05, NORMX=0.333, NORMY=0.428, R=0.761, THETA=0.579, X=4554, Y=2131}]] filters=
18:12:28.994 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178902506 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=928, GC_SCORE=0.893, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178902506, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=28, N_BB=1220, PROBE_A=TTATTGGACCAGCCTAGACTGAAAATCTTCTGTTTAGGCATTTTGGTGGG, PROBE_B=., SOURCE=psych, devR_AA=0.1, devR_AB=0.105, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.023, devTHETA_BB=0.01, devX_AA=0.101, devX_AB=0.054, devX_BB=0.015, devY_AA=0.031, devY_AB=0.055, devY_BB=0.097, meanR_AA=0.948, meanR_AB=1.181, meanR_BB=0.994, meanTHETA_AA=0.026, meanTHETA_AB=0.512, meanTHETA_BB=0.973, meanX_AA=0.911, meanX_AB=0.58, meanX_BB=0.041, meanY_AA=0.037, meanY_AB=0.602, meanY_BB=0.953, refSNP=rs111868222, zthresh_X=0.140378981558, zthresh_Y=0.166929562077} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.99, GTA=0/0, GTZ=0/0, IGC=0.882, LRR=0.069, NORMX=0.057, NORMY=0.99, R=1.047, THETA=0.963, X=1498, Y=5593}]] filters=
18:12:28.994 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178907849 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.797, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178907849, ILLUMINA_STRAND=TOP, N_AA=19, N_AB=360, N_BB=872, PROBE_A=GAGGCCCTAACTGGGGCCCAGAAAATTGTACTGAAGGATACTTGCTTCCT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.023, devTHETA_AB=0.038, devTHETA_BB=0.021, devX_AA=0.094, devX_AB=0.05, devX_BB=0.018, devY_AA=0.019, devY_AB=0.056, devY_BB=0.093, meanR_AA=0.556, meanR_AB=0.58, meanR_BB=0.576, meanTHETA_AA=0.054, meanTHETA_AB=0.544, meanTHETA_BB=0.94, meanX_AA=0.513, meanX_AB=0.27, meanX_BB=0.05, meanY_AA=0.043, meanY_AB=0.31, meanY_BB=0.526, refSNP=rs9866361, zthresh_X=0.161949964118, zthresh_Y=0.175918019742} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.978, GTA=0/0, GTZ=0/0, IGC=0.811, LRR=-0.054, NORMX=0.061, NORMY=0.495, R=0.555, THETA=0.922, X=1038, Y=2429}]] filters=
18:12:28.994 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916753 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.886, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916753, ILLUMINA_STRAND=TOP, N_AA=1247, N_AB=0, N_BB=0, PROBE_A=GATAGTGACTTTAGAATGCCTCCGTGAGGCTACATTAATAACCATAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.094, devX_AB=0.05, devX_BB=0.017, devY_AA=0.015, devY_AB=0.052, devY_BB=0.098, meanR_AA=0.455, meanR_AB=0.541, meanR_BB=0.503, meanTHETA_AA=0.047, meanTHETA_AB=0.511, meanTHETA_BB=0.976, meanX_AA=0.424, meanX_AB=0.266, meanX_BB=0.018, meanY_AA=0.031, meanY_AB=0.275, meanY_BB=0.485, refSNP=rs190372148, zthresh_X=0.182850738152, zthresh_Y=0.12847847542} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.489, LRR=0.114, NORMX=0.459, NORMY=0.034, R=0.493, THETA=0.047, X=8065, Y=228}]] filters=
18:12:28.995 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916791 Q. of type=SNP alleles=[C*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.89, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916791, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TAACCATAAAGCATGAACTATTTAAAGAAGCAAGAAAATACCCCCTCCAT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.013, devX_AA=0.099, devX_AB=0.053, devX_BB=0.014, devY_AA=0.024, devY_AB=0.052, devY_BB=0.096, meanR_AA=0.738, meanR_AB=0.886, meanR_BB=0.745, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.965, meanX_AA=0.711, meanX_AB=0.447, meanX_BB=0.039, meanY_AA=0.027, meanY_AB=0.439, meanY_BB=0.706, refSNP=rs71310379, zthresh_X=0.133750336661, zthresh_Y=0.164321280546} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.494, LRR=0.001, NORMX=0.022, NORMY=0.718, R=0.741, THETA=0.98, X=620, Y=4057}]] filters=
18:12:28.995 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178921158 Q. of type=SNP alleles=[G*, A] attr={AC=1, AF=0.500, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.788, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178921158, ILLUMINA_STRAND=TOP, N_AA=30, N_AB=414, N_BB=807, PROBE_A=CTTTCGTGCAATTTATATTCAGAAGTGTTTGATTGATCTTGTGCTTCAAC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.016, devTHETA_AB=0.029, devTHETA_BB=0.015, devX_AA=0.094, devX_AB=0.049, devX_BB=0.021, devY_AA=0.019, devY_AB=0.061, devY_BB=0.092, meanR_AA=0.827, meanR_AB=0.983, meanR_BB=0.947, meanTHETA_AA=0.05, meanTHETA_AB=0.585, meanTHETA_BB=0.933, meanX_AA=0.767, meanX_AB=0.426, meanX_BB=0.09, meanY_AA=0.06, meanY_AB=0.557, meanY_BB=0.857, refSNP=rs7623154, zthresh_X=0.224662521322, zthresh_Y=0.204527740428} GT=[[0816201804HC0_R01C01 G*/A {BAF=0.484, GTA=1/0, GTZ=1/0, IGC=0.797, LRR=0.017, NORMX=0.442, NORMY=0.547, R=0.99, THETA=0.567, X=6004, Y=2730}]] filters=
18:12:28.996 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 Q. of type=SNP alleles=[C*, G] attr={AC=0, AF=0.00, ALLELE_A=G, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178922361, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1249, PROBE_A=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACG, PROBE_B=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACC, SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.014, devX_AA=0.099, devX_AB=0.052, devX_BB=0.014, devY_AA=0.022, devY_AB=0.052, devY_BB=0.097, meanR_AA=0.664, meanR_AB=0.793, meanR_BB=0.678, meanTHETA_AA=0.024, meanTHETA_AB=0.501, meanTHETA_BB=0.977, meanX_AA=0.64, meanX_AB=0.396, meanX_BB=0.024, meanY_AA=0.025, meanY_AB=0.397, meanY_BB=0.654, refSNP=rs113613074, zthresh_X=0.119568794798, zthresh_Y=0.156845592246} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.515, LRR=-0.048, NORMX=0.015, NORMY=0.639, R=0.654, THETA=0.986, X=603, Y=11188}]] filters=
18:12:28.996 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=1161, GC_SCORE=0.868, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178927410, ILLUMINA_STRAND=BOT, N_AA=1072, N_AB=169, N_BB=0, PROBE_A=GAGCAAATGGAAAGGCAAAGTCGAGCAGCACGAGGAAGATCAGGAATGTA, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.042, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.058, devX_BB=0.024, devY_AA=0.015, devY_AB=0.059, devY_BB=0.099, meanR_AA=0.829, meanR_AB=0.918, meanR_BB=0.742, meanTHETA_AA=0.017, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=0.808, meanX_AB=0.452, meanX_BB=0.028, meanY_AA=0.021, meanY_AB=0.466, meanY_BB=0.714, refSNP=rs2230461, zthresh_X=0.183044318831, zthresh_Y=0.127662818665} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.009, GTA=0/0, GTZ=0/0, IGC=0.851, LRR=0.267, NORMX=0.961, NORMY=0.038, R=1, THETA=0.025, X=15373, Y=361}]] filters=
18:12:28.996 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=971, GC_SCORE=0.869, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178932551, ILLUMINA_STRAND=TOP, N_AA=343, N_AB=398, N_BB=479, PROBE_A=GTGAAGACCTGCTGTTTTCTCTGCTTCCAAGCTCAACTAACAATATATTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.131, devR_AB=0.1, devR_BB=0.123, devTHETA_AA=0.017, devTHETA_AB=0.023, devTHETA_BB=0.022, devX_AA=0.126, devX_AB=0.061, devX_BB=0.024, devY_AA=0.017, devY_AB=0.074, devY_BB=0.118, meanR_AA=0.622, meanR_AB=0.938, meanR_BB=0.739, meanTHETA_AA=0.028, meanTHETA_AB=0.563, meanTHETA_BB=0.965, meanX_AA=0.596, meanX_AB=0.423, meanX_BB=0.038, meanY_AA=0.026, meanY_AB=0.515, meanY_BB=0.701, refSNP=rs12494623, zthresh_X=0.152176899827, zthresh_Y=0.170103096568} GT=[[0816201804HC0_R01C01 T/T {BAF=0.027, GTA=1/1, GTZ=1/1, IGC=0.906, LRR=-0.336, NORMX=0.465, NORMY=0.042, R=0.507, THETA=0.057, X=7174, Y=362}]] filters=
18:12:28.997 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.891, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178937400, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CATACACAGATGTATTGCTTGGTAAAAGATTGGCCTCCAATCAAACCTGA, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.108, devR_BB=0.1, devTHETA_AA=0.013, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.053, devX_BB=0.026, devY_AA=0.015, devY_AB=0.053, devY_BB=0.1, meanR_AA=0.79, meanR_AB=0.96, meanR_BB=0.803, meanTHETA_AA=0.031, meanTHETA_AB=0.503, meanTHETA_BB=0.976, meanX_AA=0.753, meanX_AB=0.477, meanX_BB=0.029, meanY_AA=0.037, meanY_AB=0.482, meanY_BB=0.773, refSNP=rs137902538, zthresh_X=0.187164813479, zthresh_Y=0.140282002247} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.496, LRR=-0.05, NORMX=0.731, NORMY=0.031, R=0.761, THETA=0.027, X=12748, Y=231}]] filters=
18:12:28.997 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.902, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178947118, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=ACCTTTCAAGCCGCCTTTGCACTGAATTTGCATAATAGTGTGAGAATTTC, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.098, devX_AB=0.052, devX_BB=0.014, devY_AA=0.019, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.576, meanR_AB=0.681, meanR_BB=0.596, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.964, meanX_AA=0.555, meanX_AB=0.344, meanX_BB=0.032, meanY_AA=0.021, meanY_AB=0.337, meanY_BB=0.565, zthresh_X=0.122228724787, zthresh_Y=0.159007429626} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.509, LRR=0.03, NORMX=0.022, NORMY=0.585, R=0.607, THETA=0.977, X=711, Y=3117}]] filters=
18:12:28.997 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.848, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178950297, ILLUMINA_STRAND=BOT, N_AA=486, N_AB=560, N_BB=205, PROBE_A=GTCTGTGTGTCTGCTTTTGTGTGTATCTGCTGTTTTGGTAATTATAGTTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.102, devR_AB=0.12, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.028, devTHETA_BB=0.016, devX_AA=0.099, devX_AB=0.057, devX_BB=0.022, devY_AA=0.018, devY_AB=0.057, devY_BB=0.094, meanR_AA=1.064, meanR_AB=1.186, meanR_BB=1.006, meanTHETA_AA=0.03, meanTHETA_AB=0.494, meanTHETA_BB=0.943, meanX_AA=1.016, meanX_AB=0.598, meanX_BB=0.083, meanY_AA=0.048, meanY_AB=0.587, meanY_BB=0.923, refSNP=rs1607237, zthresh_X=0.199217026256, zthresh_Y=0.172626912202} GT=[[0816201804HC0_R01C01 T/T {BAF=0, GTA=1/1, GTZ=1/1, IGC=0.882, LRR=-0.014, NORMX=1.013, NORMY=0.039, R=1.052, THETA=0.025, X=13288, Y=291}]] filters=
18:12:28.998 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.832, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960744, ILLUMINA_STRAND=BOT, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=AAGATTTCTCTGCTCTTCCTTTGCTCCTCCTCATAATGCACAGTTTGAAC, PROBE_B=., SOURCE=1000_genomes, devR_AA=0.1, devR_AB=0.195, devR_BB=0.113, devTHETA_AA=0.007, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.059, devX_BB=0.042, devY_AA=0.015, devY_AB=0.058, devY_BB=0.117, meanR_AA=1.388, meanR_AB=1.725, meanR_BB=1.296, meanTHETA_AA=0.014, meanTHETA_AB=0.495, meanTHETA_BB=0.975, meanX_AA=1.358, meanX_AB=0.87, meanX_BB=0.048, meanY_AA=0.029, meanY_AB=0.855, meanY_BB=1.248, refSNP=rs200646413, zthresh_X=0.181538312311, zthresh_Y=0.124907131052} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0.004, GTA=0/0, GTZ=0/0, IGC=0.423, LRR=0.033, NORMX=1.384, NORMY=0.039, R=1.423, THETA=0.018, X=24000, Y=330}]] filters=
18:12:28.998 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.847, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960843, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.18, devR_BB=0.106, devTHETA_AA=0.009, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.057, devX_BB=0.04, devY_AA=0.017, devY_AB=0.058, devY_BB=0.11, meanR_AA=1.287, meanR_AB=1.594, meanR_BB=1.215, meanTHETA_AA=0.034, meanTHETA_AB=0.505, meanTHETA_BB=0.976, meanX_AA=1.221, meanX_AB=0.791, meanX_BB=0.044, meanY_AA=0.066, meanY_AB=0.804, meanY_BB=1.171, refSNP=rs145985409, zthresh_X=0.19811140407, zthresh_Y=0.172079887333} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.01, GTA=0/0, GTZ=0/0, IGC=0.441, LRR=0.077, NORMX=1.276, NORMY=0.087, R=1.363, THETA=0.043, X=22154, Y=590}]] filters=
18:12:28.998 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.901, ILLUMINA_BUILD=37.2, ILLUMINA_CHR=3, ILLUMINA_POS=178962380, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=CGACTGGCTGGACTGTGCCTTCACCTGTGGTGTGCACTGCCACGGTCAGG, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.133, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.009, devX_AA=0.101, devX_AB=0.054, devX_BB=0.013, devY_AA=0.032, devY_AB=0.054, devY_BB=0.097, meanR_AA=0.964, meanR_AB=1.179, meanR_BB=0.948, meanTHETA_AA=0.024, meanTHETA_AB=0.5, meanTHETA_BB=0.976, meanX_AA=0.928, meanX_AB=0.589, meanX_BB=0.034, meanY_AA=0.036, meanY_AB=0.59, meanY_BB=0.915, refSNP=rs199686819, zthresh_X=0.12173904259, zthresh_Y=0.159179424244} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.508, LRR=-0.062, NORMX=0.033, NORMY=0.876, R=0.909, THETA=0.976, X=819, Y=4947}]] filters=
18:12:28.998 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.879, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178962425, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=GAGAGAAGAATCGACCTGCACTGCCATCCACACAGATATCATGGACGACT, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.121, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.011, devX_AA=0.101, devX_AB=0.054, devX_BB=0.014, devY_AA=0.029, devY_AB=0.053, devY_BB=0.095, meanR_AA=0.883, meanR_AB=1.074, meanR_BB=0.877, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.851, meanX_AB=0.543, meanX_BB=0.048, meanY_AA=0.032, meanY_AB=0.532, meanY_BB=0.829, refSNP=rs145138176, zthresh_X=0.14237441016, zthresh_Y=0.168724424863} GT=[[0816201804HC0_R01C01 C*/C* {BAF=0.999, GTA=0/0, GTZ=0/0, IGC=0.48, LRR=-0.121, NORMX=0.045, NORMY=0.761, R=0.806, THETA=0.963, X=1125, Y=4047}]] filters=
18:12:28.998 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968543 Q. of type=SNP alleles=[G*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968543, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=1, N_BB=1250, PROBE_A=GGGCTTCTCAGTCCTAATGTTCTTCTTGCTCGGAACAACCATTCTAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.104, devR_AB=0.156, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.008, devX_AA=0.107, devX_AB=0.058, devX_BB=0.014, devY_AA=0.036, devY_AB=0.057, devY_BB=0.097, meanR_AA=1.1, meanR_AB=1.381, meanR_BB=1.127, meanTHETA_AA=0.025, meanTHETA_AB=0.492, meanTHETA_BB=0.975, meanX_AA=1.059, meanX_AB=0.7, meanX_BB=0.042, meanY_AA=0.041, meanY_AB=0.682, meanY_BB=1.085, refSNP=rs61734056, zthresh_X=0.135160960006, zthresh_Y=0.165299195841} GT=[[0816201804HC0_R01C01 G*/G* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.897, LRR=0.034, NORMX=0.04, NORMY=1.113, R=1.153, THETA=0.977, X=972, Y=6285}]] filters=
18:12:28.999 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968568 Q. of type=SNP alleles=[A*, C] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=C, AN=2, BEADSET_ID=1168, GC_SCORE=0.889, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968568, ILLUMINA_STRAND=BOT, N_AA=1249, N_AB=1, N_BB=0, PROBE_A=CCGTGATGCTGGGGTTTGCCATGATGGGCTTCTCAGTCCTAATGTTCTTC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.143, devR_AB=0.175, devR_BB=0.109, devTHETA_AA=0.01, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.14, devX_AB=0.076, devX_BB=0.041, devY_AA=0.016, devY_AB=0.077, devY_BB=0.113, meanR_AA=1.113, meanR_AB=1.547, meanR_BB=1.25, meanTHETA_AA=0.019, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=1.081, meanX_AB=0.763, meanX_BB=0.046, meanY_AA=0.032, meanY_AB=0.784, meanY_BB=1.204, refSNP=rs2276802, zthresh_X=0.189602852188, zthresh_Y=0.145988814983} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.878, LRR=-0.023, NORMX=1.069, NORMY=0.021, R=1.089, THETA=0.012, X=17958, Y=362}]] filters=
18:12:28.999 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968634 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.885, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968634, ILLUMINA_STRAND=TOP, N_AA=216, N_AB=596, N_BB=439, PROBE_A=ACTACAGTGATGGAGACCCACTAGATGTGCACAAGAGGCTGCCATCCAGT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.011, devTHETA_AB=0.025, devTHETA_BB=0.01, devX_AA=0.096, devX_AB=0.058, devX_BB=0.015, devY_AA=0.019, devY_AB=0.054, devY_BB=0.097, meanR_AA=1.156, meanR_AB=1.266, meanR_BB=0.992, meanTHETA_AA=0.036, meanTHETA_AB=0.47, meanTHETA_BB=0.972, meanX_AA=1.094, meanX_AB=0.662, meanX_BB=0.042, meanY_AA=0.062, meanY_AB=0.603, meanY_BB=0.951, refSNP=rs7645550, zthresh_X=0.139062088415, zthresh_Y=0.166539592425} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.496, GTA=1/0, GTZ=1/0, IGC=0.922, LRR=-0.041, NORMX=0.647, NORMY=0.582, R=1.23, THETA=0.466, X=11372, Y=3338}]] filters=
18:12:28.999 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968660 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.862, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968660, ILLUMINA_STRAND=TOP, N_AA=987, N_AB=246, N_BB=18, PROBE_A=TGCCTCAGGGAAGAAGAGAGAGACAGACTACAGTGATGGAGACCCACTAG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.01, devTHETA_AB=0.039, devTHETA_BB=0.016, devX_AA=0.096, devX_AB=0.061, devX_BB=0.022, devY_AA=0.015, devY_AB=0.061, devY_BB=0.098, meanR_AA=1.016, meanR_AB=1.151, meanR_BB=0.92, meanTHETA_AA=0.036, meanTHETA_AB=0.5, meanTHETA_BB=0.97, meanX_AA=0.962, meanX_AB=0.575, meanX_BB=0.041, meanY_AA=0.054, meanY_AB=0.576, meanY_BB=0.878, refSNP=rs1170672, zthresh_X=0.191295862566, zthresh_Y=0.153061435119} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.899, LRR=0.047, NORMX=1.001, NORMY=0.046, R=1.048, THETA=0.029, X=17415, Y=341}]] filters=
18:12:28.999 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968848 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.884, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968848, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TATTTAGATGGACTTTTCACCAAGCTCTGAACTGGGATTTCATTTTGTTG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.099, devX_AB=0.052, devX_BB=0.015, devY_AA=0.022, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.662, meanR_AB=0.79, meanR_BB=0.676, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.638, meanX_AB=0.399, meanX_BB=0.037, meanY_AA=0.024, meanY_AB=0.391, meanY_BB=0.639, refSNP=rs113011029, zthresh_X=0.138051204865, zthresh_Y=0.165472197716} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.988, GTA=0/0, GTZ=0/0, IGC=0.486, LRR=0.095, NORMX=0.051, NORMY=0.674, R=0.725, THETA=0.952, X=1106, Y=3811}]] filters=
18:12:28.999 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
18:12:28.999 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:12:28.999 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
18:12:29.000 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:29.070 INFO  Funcotator - ------------------------------------------------------------
18:12:29.070 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:29.070 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:29.070 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:29.070 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:29.070 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:29 PM UTC
18:12:29.070 INFO  Funcotator - ------------------------------------------------------------
18:12:29.070 INFO  Funcotator - ------------------------------------------------------------
18:12:29.070 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:29.070 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:29.070 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:29.070 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:29.070 INFO  Funcotator - Deflater: IntelDeflater
18:12:29.070 INFO  Funcotator - Inflater: IntelInflater
18:12:29.070 INFO  Funcotator - GCS max retries/reopens: 20
18:12:29.070 INFO  Funcotator - Requester pays: disabled
18:12:29.070 INFO  Funcotator - Initializing engine
18:12:29.071 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
18:12:29.072 INFO  Funcotator - Done initializing engine
18:12:29.072 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:29.072 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:29.072 INFO  Funcotator - Initializing data sources...
18:12:29.072 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
18:12:29.072 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:29.072 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.072 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.072 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:29.072 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:29.072 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:12:29.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.073 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
18:12:29.100 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.100 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:12:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:12:29.101 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.101 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:29.101 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.102 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:29.102 INFO  Funcotator - Initializing Funcotator Engine...
18:12:29.102 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:12:29.102 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:12:29.102 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6960020105923659633.vcf
18:12:29.105 INFO  ProgressMeter - Starting traversal
18:12:29.105 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:29.109 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
18:12:29.109 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
18:12:29.109 WARN  Funcotator - ================================================================================
18:12:29.109 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:12:29.109 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:12:29.109 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:12:29.109 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:12:29.109 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:12:29.109 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:12:29.109 WARN  Funcotator - --------------------------------------------------------------------------------
18:12:29.109 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:12:29.109 WARN  Funcotator -  run was misconfigured.     
18:12:29.109 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:12:29.109 WARN  Funcotator - ================================================================================
18:12:29.110 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:29.110 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6960020105923659633.vcf
18:12:29.185 INFO  Funcotator - ------------------------------------------------------------
18:12:29.185 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
18:12:29.185 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:12:29.185 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:12:29.185 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:12:29.185 INFO  Funcotator - Start Date/Time: May 27, 2025 at 6:12:29 PM UTC
18:12:29.185 INFO  Funcotator - ------------------------------------------------------------
18:12:29.185 INFO  Funcotator - ------------------------------------------------------------
18:12:29.185 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:12:29.185 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:12:29.185 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:12:29.185 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:12:29.185 INFO  Funcotator - Deflater: IntelDeflater
18:12:29.185 INFO  Funcotator - Inflater: IntelInflater
18:12:29.185 INFO  Funcotator - GCS max retries/reopens: 20
18:12:29.185 INFO  Funcotator - Requester pays: disabled
18:12:29.185 INFO  Funcotator - Initializing engine
18:12:29.187 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
18:12:29.189 INFO  Funcotator - Done initializing engine
18:12:29.189 INFO  Funcotator - Skipping sequence dictionary validation.
18:12:29.189 INFO  Funcotator - Processing user transcripts/defaults/overrides...
18:12:29.189 INFO  Funcotator - Initializing data sources...
18:12:29.189 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
18:12:29.189 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
18:12:29.190 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.190 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.190 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:29.190 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
18:12:29.190 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
18:12:29.191 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.191 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
18:12:29.226 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
18:12:29.227 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 18:12:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
18:12:29.227 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.227 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
18:12:29.227 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
18:12:29.228 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
18:12:29.228 INFO  Funcotator - Initializing Funcotator Engine...
18:12:29.228 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
18:12:29.228 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
18:12:29.228 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16646006384462689373.vcf
18:12:29.231 INFO  ProgressMeter - Starting traversal
18:12:29.231 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:12:29.233 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
18:12:29.233 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
18:12:29.233 WARN  Funcotator - ================================================================================
18:12:29.233 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
18:12:29.233 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
18:12:29.233 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
18:12:29.233 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
18:12:29.233 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
18:12:29.233 WARN  Funcotator -                                                   |___/                         ?[0;0m
18:12:29.233 WARN  Funcotator - --------------------------------------------------------------------------------
18:12:29.233 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
18:12:29.233 WARN  Funcotator -  run was misconfigured.     
18:12:29.233 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
18:12:29.233 WARN  Funcotator - ================================================================================
18:12:29.234 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 6:12:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
18:12:29.234 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16646006384462689373.vcf