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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
tests
failures
ignored
1m47.04s
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/funcotatorTmpFolder13863599965694014468/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)	1.186s	passed
exhaustiveArgumentTest[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.372s	passed
exhaustiveArgumentTest[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	1.034s	passed
exhaustiveArgumentTest[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.114s	passed
exhaustiveArgumentTest[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	1.077s	passed
exhaustiveArgumentTest[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.154s	passed
exhaustiveArgumentTest[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	1.088s	passed
exhaustiveArgumentTest[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.059s	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)	6.576s	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)	5.816s	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)	2.011s	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)	1.949s	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)	13.232s	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)	6.227s	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)	0.077s	passed
testCanAnnotateHg38ClinvarAndGencodeV28	0.185s	passed
testCanAnnotateMixedContigHg19Clinvar	0.099s	passed
testCanAnnotateSpanningDeletions	0.159s	passed
testCanCreateNonLocatableFuncotations	0.999s	passed
testCanHandleSymbollicAlleleFuncotations	1.122s	passed
testCustomVariantClassificationOrder	1.044s	passed
testEColiFuncotations	0.104s	passed
testEnsureDbSnpInMaf	0.078s	passed
testExclusionFromDatasourceVcfToVcf	0.177s	passed
testFilterParsing	0.113s	passed
testFuncotatorWithoutValidatingResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	0.942s	passed
testFuncotatorWithoutValidatingResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.034s	passed
testFuncotatorWithoutValidatingResults[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	0.984s	passed
testFuncotatorWithoutValidatingResults[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.046s	passed
testFuncotatorWithoutValidatingResults[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	0.979s	passed
testFuncotatorWithoutValidatingResults[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.098s	passed
testFuncotatorWithoutValidatingResults[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder13863599965694014468/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)	0.962s	passed
testFuncotatorWithoutValidatingResults[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder14956303455277940652/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)	1.093s	passed
testMANESelectAnnotationDifferencesAndGencodeV43	0.381s	passed
testMafCustomCountFieldsTumorOnly[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf)	0.084s	passed
testMafCustomCountFieldsTumorOnly[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf)	0.083s	passed
testMafCustomCountFields[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf)	0.087s	passed
testMafCustomCountFields[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf)	0.084s	passed
testManualAnnotationsCorrectness	0.095s	passed
testMoreThanOneTNPair	0.078s	passed
testNoSpanningDeletionWriteWithMAF	0.136s	passed
testNoVariantsProduceMaf	0.077s	passed
testSequenceDictionaryCheck	0.073s	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)	6.281s	passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput	0.848s	passed
testVCFColumnsArentShuffled	0.083s	passed
testVCFToMAFPreservesFields	0.091s	passed
testVCFToVCFPreservesFields	0.097s	passed
testVcfDatasourceAccountsForAltAlleles	0.087s	passed
testVcfMafConcordance[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder10651368768008399516/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15)	0.172s	passed
testVcfMafConcordance[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder10651368768008399516/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.224s	passed
testVcfMafConcordance[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder14956303455277940652/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057)	39.858s	passed
testVcfMafConcordance[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder7286131020602952051/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)	0.367s	passed
testVcfMafConcordance[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder10651368768008399516/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)	0.248s	passed
testVcfToMafHonorsExcludedFields	0.091s	passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified	0.113s	passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations	0.111s	passed
Standard error

14:17:04.862 INFO  Funcotator - ------------------------------------------------------------
14:17:04.862 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:04.862 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:04.862 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:04.862 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:04.862 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:04 PM UTC
14:17:04.862 INFO  Funcotator - ------------------------------------------------------------
14:17:04.862 INFO  Funcotator - ------------------------------------------------------------
14:17:04.863 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:04.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:04.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:04.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:04.863 INFO  Funcotator - Deflater: IntelDeflater
14:17:04.863 INFO  Funcotator - Inflater: IntelInflater
14:17:04.863 INFO  Funcotator - GCS max retries/reopens: 20
14:17:04.863 INFO  Funcotator - Requester pays: disabled
14:17:04.863 INFO  Funcotator - Initializing engine
14:17:04.864 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
14:17:04.865 INFO  Funcotator - Done initializing engine
14:17:04.865 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:04.865 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:04.865 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13225026068623041117/TranscriptIdFile.txt
14:17:04.866 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:17:04.866 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:04.866 INFO  Funcotator - Initializing data sources...
14:17:04.866 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:04.866 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:04.866 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
14:17:04.867 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
14:17:04.867 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
14:17:04.867 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
14:17:04.867 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
14:17:04.867 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
14:17:04.868 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
14:17:04.868 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
14:17:04.868 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
14:17:04.868 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
14:17:04.868 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
14:17:04.869 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
14:17:04.869 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
14:17:04.869 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
14:17:04.869 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
14:17:04.869 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:04.870 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
14:17:04.956 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
14:17:04.999 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
14:17:05.049 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
14:17:05.056 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
14:17:05.057 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
14:17:05.057 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
14:17:05.057 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
14:17:05.672 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
14:17:05.711 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
14:17:05.711 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:05.712 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
14:17:05.712 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
14:17:05.807 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:05.807 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
14:17:05.808 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
14:17:05.844 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
14:17:05.844 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	2025-06-02 14:17:05	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:05.845 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
14:17:05.845 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
14:17:05.846 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
14:17:05.846 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:05.847 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
14:17:05.849 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
14:17:05.852 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
14:17:05.854 INFO  Funcotator - Initializing Funcotator Engine...
14:17:05.854 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
14:17:05.855 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:05.855 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:05.855 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:05.855 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:05.856 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:05.857 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:05.858 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:05.858 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:05.858 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.312599871372622007479.vcf
14:17:05.858 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
14:17:05.862 INFO  ProgressMeter - Starting traversal
14:17:05.862 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:05.972 INFO  ProgressMeter -             unmapped              0.0                     3           1636.4
14:17:05.972 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:05.972 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:05.976 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:05 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2743074816
14:17:06.048 INFO  Funcotator - ------------------------------------------------------------
14:17:06.048 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:06.048 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:06.048 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:06.048 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:06.048 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:06 PM UTC
14:17:06.048 INFO  Funcotator - ------------------------------------------------------------
14:17:06.048 INFO  Funcotator - ------------------------------------------------------------
14:17:06.048 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:06.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:06.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:06.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:06.048 INFO  Funcotator - Deflater: IntelDeflater
14:17:06.048 INFO  Funcotator - Inflater: IntelInflater
14:17:06.048 INFO  Funcotator - GCS max retries/reopens: 20
14:17:06.048 INFO  Funcotator - Requester pays: disabled
14:17:06.048 INFO  Funcotator - Initializing engine
14:17:06.050 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
14:17:06.051 INFO  Funcotator - Done initializing engine
14:17:06.051 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:06.051 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:06.051 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder5036047128448256663/TranscriptIdFile.txt
14:17:06.051 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:17:06.051 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:06.051 INFO  Funcotator - Initializing data sources...
14:17:06.051 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:06.051 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:06.051 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
14:17:06.052 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
14:17:06.052 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
14:17:06.052 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
14:17:06.052 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
14:17:06.053 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
14:17:06.053 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
14:17:06.053 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
14:17:06.053 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
14:17:06.054 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
14:17:06.054 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
14:17:06.054 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
14:17:06.054 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
14:17:06.054 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
14:17:06.055 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
14:17:06.055 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:06.055 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
14:17:06.055 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
14:17:06.098 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
14:17:06.116 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
14:17:06.123 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
14:17:06.123 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
14:17:06.123 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
14:17:06.124 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
14:17:06.753 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
14:17:06.794 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
14:17:06.795 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:06.796 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
14:17:06.796 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
14:17:06.895 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:06.895 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
14:17:06.896 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
14:17:06.924 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
14:17:06.924 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	2025-06-02 14:17:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:06.924 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
14:17:06.925 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
14:17:06.925 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
14:17:06.925 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:06.926 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
14:17:06.928 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
14:17:06.933 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
14:17:06.937 INFO  Funcotator - Initializing Funcotator Engine...
14:17:06.937 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:06.937 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:06.937 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.417806928315040023368.vcf
14:17:06.939 INFO  ProgressMeter - Starting traversal
14:17:06.939 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:07.347 INFO  ProgressMeter -             unmapped              0.0                     4            588.2
14:17:07.347 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:07.347 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:07.348 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2743074816
14:17:07.421 INFO  Funcotator - ------------------------------------------------------------
14:17:07.421 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:07.421 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:07.421 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:07.421 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:07.421 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:07 PM UTC
14:17:07.421 INFO  Funcotator - ------------------------------------------------------------
14:17:07.421 INFO  Funcotator - ------------------------------------------------------------
14:17:07.421 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:07.421 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:07.421 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:07.421 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:07.421 INFO  Funcotator - Deflater: IntelDeflater
14:17:07.421 INFO  Funcotator - Inflater: IntelInflater
14:17:07.421 INFO  Funcotator - GCS max retries/reopens: 20
14:17:07.421 INFO  Funcotator - Requester pays: disabled
14:17:07.421 INFO  Funcotator - Initializing engine
14:17:07.422 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
14:17:07.423 INFO  Funcotator - Done initializing engine
14:17:07.423 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:07.423 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:07.423 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder1086861027002929021/TranscriptIdFile.txt
14:17:07.423 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:17:07.423 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:07.423 INFO  Funcotator - Initializing data sources...
14:17:07.423 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:07.423 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:07.423 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
14:17:07.424 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
14:17:07.424 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
14:17:07.424 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
14:17:07.424 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
14:17:07.425 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
14:17:07.425 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
14:17:07.425 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
14:17:07.425 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
14:17:07.425 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
14:17:07.425 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
14:17:07.425 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
14:17:07.426 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
14:17:07.426 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
14:17:07.426 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
14:17:07.426 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:07.426 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
14:17:07.427 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
14:17:07.468 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
14:17:07.487 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
14:17:07.494 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
14:17:07.494 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
14:17:07.495 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
14:17:07.495 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
14:17:08.146 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
14:17:08.185 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
14:17:08.185 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:08.186 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
14:17:08.187 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
14:17:08.271 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:08.271 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
14:17:08.272 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
14:17:08.301 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
14:17:08.301 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	2025-06-02 14:17:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:08.301 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
14:17:08.302 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
14:17:08.302 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
14:17:08.302 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:08.303 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
14:17:08.338 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
14:17:08.342 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
14:17:08.344 INFO  Funcotator - Initializing Funcotator Engine...
14:17:08.344 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
14:17:08.345 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:08.345 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:08.345 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:08.345 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:08.346 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:08.346 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:08.346 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.312220833107084491900.vcf
14:17:08.346 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
14:17:08.347 INFO  ProgressMeter - Starting traversal
14:17:08.347 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:08.378 INFO  ProgressMeter -             unmapped              0.0                     3           5806.5
14:17:08.379 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:08.379 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:08.382 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:08 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2820669440
14:17:08.459 INFO  Funcotator - ------------------------------------------------------------
14:17:08.459 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:08.459 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:08.459 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:08.459 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:08.459 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:08 PM UTC
14:17:08.459 INFO  Funcotator - ------------------------------------------------------------
14:17:08.459 INFO  Funcotator - ------------------------------------------------------------
14:17:08.459 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:08.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:08.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:08.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:08.459 INFO  Funcotator - Deflater: IntelDeflater
14:17:08.459 INFO  Funcotator - Inflater: IntelInflater
14:17:08.459 INFO  Funcotator - GCS max retries/reopens: 20
14:17:08.459 INFO  Funcotator - Requester pays: disabled
14:17:08.459 INFO  Funcotator - Initializing engine
14:17:08.460 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
14:17:08.461 INFO  Funcotator - Done initializing engine
14:17:08.461 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:08.461 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:08.461 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder16824647384091386853/TranscriptIdFile.txt
14:17:08.461 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:17:08.461 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:08.461 INFO  Funcotator - Initializing data sources...
14:17:08.461 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:08.461 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:08.462 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
14:17:08.462 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
14:17:08.462 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
14:17:08.462 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
14:17:08.463 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
14:17:08.463 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
14:17:08.463 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
14:17:08.463 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
14:17:08.463 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
14:17:08.464 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
14:17:08.464 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
14:17:08.464 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
14:17:08.464 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
14:17:08.464 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
14:17:08.465 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
14:17:08.465 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:08.465 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
14:17:08.465 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
14:17:08.508 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
14:17:08.526 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
14:17:08.532 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
14:17:08.533 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
14:17:08.533 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
14:17:08.533 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
14:17:09.173 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
14:17:09.212 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
14:17:09.212 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:09.213 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
14:17:09.213 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
14:17:09.296 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:09.297 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
14:17:09.297 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
14:17:09.325 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
14:17:09.325 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	2025-06-02 14:17:09	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:09.325 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
14:17:09.326 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
14:17:09.326 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
14:17:09.326 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:09.327 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
14:17:09.329 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
14:17:09.331 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
14:17:09.334 INFO  Funcotator - Initializing Funcotator Engine...
14:17:09.334 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:09.334 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:09.334 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.413623910223036233652.vcf
14:17:09.335 INFO  ProgressMeter - Starting traversal
14:17:09.335 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:09.496 INFO  ProgressMeter -             unmapped              0.0                     4           1490.7
14:17:09.496 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:09.496 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:09.497 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2820669440
14:17:09.566 INFO  Funcotator - ------------------------------------------------------------
14:17:09.566 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:09.566 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:09.566 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:09.566 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:09.566 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:09 PM UTC
14:17:09.566 INFO  Funcotator - ------------------------------------------------------------
14:17:09.566 INFO  Funcotator - ------------------------------------------------------------
14:17:09.566 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:09.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:09.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:09.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:09.566 INFO  Funcotator - Deflater: IntelDeflater
14:17:09.566 INFO  Funcotator - Inflater: IntelInflater
14:17:09.566 INFO  Funcotator - GCS max retries/reopens: 20
14:17:09.566 INFO  Funcotator - Requester pays: disabled
14:17:09.566 INFO  Funcotator - Initializing engine
14:17:09.567 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
14:17:09.567 INFO  Funcotator - Done initializing engine
14:17:09.567 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:09.567 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:09.567 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder15616990891146838991/TranscriptIdFile.txt
14:17:09.567 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:17:09.567 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:09.567 INFO  Funcotator - Initializing data sources...
14:17:09.567 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:09.567 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:09.568 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
14:17:09.568 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
14:17:09.568 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
14:17:09.568 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
14:17:09.568 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
14:17:09.569 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
14:17:09.569 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
14:17:09.569 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
14:17:09.569 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
14:17:09.569 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
14:17:09.570 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
14:17:09.570 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
14:17:09.570 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
14:17:09.570 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
14:17:09.570 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
14:17:09.570 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:09.570 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
14:17:09.571 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
14:17:09.612 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
14:17:09.709 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
14:17:09.716 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
14:17:09.717 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
14:17:09.717 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
14:17:09.717 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
14:17:10.342 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
14:17:10.381 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
14:17:10.381 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:10.382 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
14:17:10.383 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
14:17:10.466 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:10.466 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
14:17:10.467 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
14:17:10.494 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
14:17:10.494 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	2025-06-02 14:17:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:10.495 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
14:17:10.495 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
14:17:10.496 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
14:17:10.496 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:10.497 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
14:17:10.499 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
14:17:10.502 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
14:17:10.504 INFO  Funcotator - Initializing Funcotator Engine...
14:17:10.504 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
14:17:10.504 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:10.504 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:10.504 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:10.504 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:10.505 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:10.505 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:10.505 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.3559031065754245454.maf
14:17:10.508 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
14:17:10.510 INFO  ProgressMeter - Starting traversal
14:17:10.510 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:10.573 INFO  ProgressMeter -             unmapped              0.0                     3           2857.1
14:17:10.573 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:10.573 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:10.573 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2904555520
14:17:10.642 INFO  Funcotator - ------------------------------------------------------------
14:17:10.642 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:10.642 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:10.642 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:10.642 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:10.642 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:10 PM UTC
14:17:10.642 INFO  Funcotator - ------------------------------------------------------------
14:17:10.642 INFO  Funcotator - ------------------------------------------------------------
14:17:10.642 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:10.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:10.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:10.642 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:10.642 INFO  Funcotator - Deflater: IntelDeflater
14:17:10.642 INFO  Funcotator - Inflater: IntelInflater
14:17:10.642 INFO  Funcotator - GCS max retries/reopens: 20
14:17:10.642 INFO  Funcotator - Requester pays: disabled
14:17:10.642 INFO  Funcotator - Initializing engine
14:17:10.643 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
14:17:10.643 INFO  Funcotator - Done initializing engine
14:17:10.643 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:10.643 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:10.643 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13055788482077618200/TranscriptIdFile.txt
14:17:10.643 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:17:10.643 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:10.643 INFO  Funcotator - Initializing data sources...
14:17:10.643 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:10.643 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:10.644 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
14:17:10.644 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
14:17:10.644 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
14:17:10.644 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
14:17:10.645 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
14:17:10.645 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
14:17:10.645 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
14:17:10.645 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
14:17:10.645 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
14:17:10.645 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
14:17:10.646 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
14:17:10.646 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
14:17:10.646 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
14:17:10.646 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
14:17:10.646 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
14:17:10.646 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:10.646 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
14:17:10.647 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
14:17:10.688 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
14:17:10.749 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
14:17:10.758 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
14:17:10.758 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
14:17:10.758 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
14:17:10.759 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
14:17:11.431 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
14:17:11.471 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
14:17:11.471 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:11.476 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
14:17:11.477 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
14:17:11.559 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:11.560 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
14:17:11.560 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
14:17:11.587 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
14:17:11.587 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	2025-06-02 14:17:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:11.588 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
14:17:11.588 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
14:17:11.588 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
14:17:11.588 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:11.589 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
14:17:11.591 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
14:17:11.594 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
14:17:11.596 INFO  Funcotator - Initializing Funcotator Engine...
14:17:11.596 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:11.596 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:11.596 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.46412221334615405007.maf
14:17:11.597 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
14:17:11.599 INFO  ProgressMeter - Starting traversal
14:17:11.599 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:11.728 INFO  ProgressMeter -             unmapped              0.0                     4           1860.5
14:17:11.728 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:11.728 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:11.728 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:11 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3057647616
14:17:11.794 INFO  Funcotator - ------------------------------------------------------------
14:17:11.794 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:11.794 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:11.794 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:11.794 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:11.794 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:11 PM UTC
14:17:11.794 INFO  Funcotator - ------------------------------------------------------------
14:17:11.794 INFO  Funcotator - ------------------------------------------------------------
14:17:11.794 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:11.794 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:11.794 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:11.794 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:11.794 INFO  Funcotator - Deflater: IntelDeflater
14:17:11.794 INFO  Funcotator - Inflater: IntelInflater
14:17:11.794 INFO  Funcotator - GCS max retries/reopens: 20
14:17:11.794 INFO  Funcotator - Requester pays: disabled
14:17:11.794 INFO  Funcotator - Initializing engine
14:17:11.795 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
14:17:11.796 INFO  Funcotator - Done initializing engine
14:17:11.796 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:11.796 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:11.796 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13598749153903091758/TranscriptIdFile.txt
14:17:11.796 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:17:11.796 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:11.796 INFO  Funcotator - Initializing data sources...
14:17:11.796 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:11.796 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:11.796 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
14:17:11.796 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
14:17:11.797 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
14:17:11.797 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
14:17:11.797 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
14:17:11.797 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
14:17:11.798 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
14:17:11.798 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
14:17:11.798 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
14:17:11.798 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
14:17:11.798 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
14:17:11.799 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
14:17:11.799 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
14:17:11.799 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
14:17:11.799 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
14:17:11.799 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:11.799 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
14:17:11.800 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
14:17:11.965 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/hg19/simple_uniprot_Dec012014.tsv
14:17:12.002 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
14:17:12.015 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
14:17:12.015 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
14:17:12.016 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
14:17:12.016 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
14:17:12.591 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
14:17:12.630 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
14:17:12.630 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:12.631 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
14:17:12.669 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
14:17:12.752 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:12.752 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
14:17:12.753 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
14:17:12.780 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
14:17:12.780 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	2025-06-02 14:17:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:12.780 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
14:17:12.781 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
14:17:12.781 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
14:17:12.781 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:12.782 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
14:17:12.784 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
14:17:12.787 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
14:17:12.789 INFO  Funcotator - Initializing Funcotator Engine...
14:17:12.789 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
14:17:12.789 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:12.789 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:12.789 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:12.789 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:12.790 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:12.790 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:12.790 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.310938907091642770765.maf
14:17:12.790 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
14:17:12.792 INFO  ProgressMeter - Starting traversal
14:17:12.792 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:12.816 INFO  ProgressMeter -             unmapped              0.0                     3           7500.0
14:17:12.816 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:12.816 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:12.816 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:12 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3181379584
14:17:12.885 INFO  Funcotator - ------------------------------------------------------------
14:17:12.885 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:12.885 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:12.885 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:12.885 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:12.885 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:12 PM UTC
14:17:12.885 INFO  Funcotator - ------------------------------------------------------------
14:17:12.885 INFO  Funcotator - ------------------------------------------------------------
14:17:12.885 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:12.885 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:12.885 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:12.885 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:12.885 INFO  Funcotator - Deflater: IntelDeflater
14:17:12.885 INFO  Funcotator - Inflater: IntelInflater
14:17:12.885 INFO  Funcotator - GCS max retries/reopens: 20
14:17:12.885 INFO  Funcotator - Requester pays: disabled
14:17:12.885 INFO  Funcotator - Initializing engine
14:17:12.885 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
14:17:12.886 INFO  Funcotator - Done initializing engine
14:17:12.886 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:12.886 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:12.886 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4022971878675610220/TranscriptIdFile.txt
14:17:12.886 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:17:12.886 INFO  FuncotatorEngine - Transcript parsing complete.
14:17:12.886 INFO  Funcotator - Initializing data sources...
14:17:12.886 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:12.886 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:12.887 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
14:17:12.887 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
14:17:12.887 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
14:17:12.887 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
14:17:12.887 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
14:17:12.888 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
14:17:12.888 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
14:17:12.888 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
14:17:12.888 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
14:17:12.888 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
14:17:12.888 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
14:17:12.889 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
14:17:12.889 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
14:17:12.889 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
14:17:12.889 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
14:17:12.889 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:12.889 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
14:17:12.890 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
14:17:12.933 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
14:17:12.951 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
14:17:12.958 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
14:17:12.959 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
14:17:12.959 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
14:17:12.959 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
14:17:13.592 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
14:17:13.631 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
14:17:13.631 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:13.632 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
14:17:13.633 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
14:17:13.715 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:13.715 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
14:17:13.716 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
14:17:13.743 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
14:17:13.743 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	2025-06-02 14:17:13	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:13.744 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
14:17:13.744 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
14:17:13.744 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
14:17:13.744 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:13.745 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
14:17:13.747 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
14:17:13.750 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
14:17:13.752 INFO  Funcotator - Initializing Funcotator Engine...
14:17:13.752 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:13.752 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:13.752 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.4499652656290537304.maf
14:17:13.752 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
14:17:13.754 INFO  ProgressMeter - Starting traversal
14:17:13.754 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:13.876 INFO  ProgressMeter -             unmapped              0.0                     4           1967.2
14:17:13.876 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:13.876 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:13.876 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:13 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3181379584
14:17:13.953 INFO  Funcotator - ------------------------------------------------------------
14:17:13.953 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:13.953 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:13.953 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:13.953 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:13.953 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:13 PM UTC
14:17:13.953 INFO  Funcotator - ------------------------------------------------------------
14:17:13.953 INFO  Funcotator - ------------------------------------------------------------
14:17:13.953 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:13.953 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:13.953 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:13.953 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:13.953 INFO  Funcotator - Deflater: IntelDeflater
14:17:13.953 INFO  Funcotator - Inflater: IntelInflater
14:17:13.953 INFO  Funcotator - GCS max retries/reopens: 20
14:17:13.953 INFO  Funcotator - Requester pays: disabled
14:17:13.953 INFO  Funcotator - Initializing engine
14:17:13.956 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
14:17:13.957 INFO  Funcotator - Done initializing engine
14:17:13.957 INFO  Funcotator - Validating sequence dictionaries...
14:17:13.957 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:13.957 INFO  Funcotator - Initializing data sources...
14:17:13.957 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:13.957 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:13.958 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
14:17:13.958 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
14:17:13.958 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
14:17:13.958 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
14:17:13.958 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
14:17:13.958 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
14:17:13.959 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
14:17:13.959 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
14:17:13.959 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
14:17:13.959 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
14:17:13.959 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
14:17:13.959 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
14:17:13.959 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
14:17:13.960 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
14:17:13.960 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
14:17:13.960 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:13.960 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
14:17:13.960 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
14:17:14.003 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
14:17:14.022 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
14:17:14.030 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
14:17:14.030 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
14:17:14.030 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
14:17:14.031 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
14:17:14.647 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
14:17:14.687 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
14:17:14.687 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:14.687 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
14:17:14.688 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
14:17:14.817 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:14.817 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
14:17:14.818 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
14:17:14.847 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
14:17:14.847 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	2025-06-02 14:17:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:14.848 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
14:17:14.848 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
14:17:14.849 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
14:17:14.849 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:14.849 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
14:17:14.851 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
14:17:14.854 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
14:17:14.856 INFO  Funcotator - Initializing Funcotator Engine...
14:17:14.856 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:14.856 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.
14:17:14.856 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11716845338565846000.vcf
14:17:14.858 INFO  ProgressMeter - Starting traversal
14:17:14.858 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:17.275 INFO  ProgressMeter -             unmapped              0.0                   198           4915.2
14:17:17.275 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:17:17.275 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:17:17.283 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:17 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3181379584
14:17:17.285 WARN  gatk -   VCF Elapsed Time: 3.406046057s
14:17:17.285 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator11716845338565846000.vcf
14:17:17.289 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
14:17:17.366 INFO  Funcotator - ------------------------------------------------------------
14:17:17.366 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:17.366 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:17.366 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:17.366 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:17.366 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:17 PM UTC
14:17:17.366 INFO  Funcotator - ------------------------------------------------------------
14:17:17.366 INFO  Funcotator - ------------------------------------------------------------
14:17:17.367 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:17.367 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:17.367 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:17.367 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:17.367 INFO  Funcotator - Deflater: IntelDeflater
14:17:17.367 INFO  Funcotator - Inflater: IntelInflater
14:17:17.367 INFO  Funcotator - GCS max retries/reopens: 20
14:17:17.367 INFO  Funcotator - Requester pays: disabled
14:17:17.367 INFO  Funcotator - Initializing engine
14:17:17.370 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
14:17:17.371 INFO  Funcotator - Done initializing engine
14:17:17.371 INFO  Funcotator - Validating sequence dictionaries...
14:17:17.372 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:17.372 INFO  Funcotator - Initializing data sources...
14:17:17.372 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:17.372 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:17.372 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
14:17:17.372 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
14:17:17.373 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
14:17:17.373 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
14:17:17.373 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
14:17:17.373 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
14:17:17.373 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
14:17:17.374 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
14:17:17.374 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
14:17:17.374 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
14:17:17.374 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
14:17:17.374 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
14:17:17.375 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
14:17:17.375 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
14:17:17.375 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
14:17:17.375 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:17.375 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
14:17:17.376 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
14:17:17.423 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
14:17:17.441 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
14:17:17.448 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
14:17:17.448 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
14:17:17.448 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
14:17:17.449 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
14:17:18.081 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
14:17:18.121 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
14:17:18.122 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:18.122 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
14:17:18.123 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
14:17:18.204 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:18.205 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
14:17:18.205 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
14:17:18.232 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
14:17:18.232 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	2025-06-02 14:17:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:18.233 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
14:17:18.233 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
14:17:18.234 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
14:17:18.234 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:18.234 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
14:17:18.236 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
14:17:18.239 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
14:17:18.242 INFO  Funcotator - Initializing Funcotator Engine...
14:17:18.242 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:18.242 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.
14:17:18.242 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator9954837656827645267.maf
14:17:18.242 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
14:17:18.244 INFO  ProgressMeter - Starting traversal
14:17:18.244 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:20.450 INFO  ProgressMeter -             unmapped              0.0                   198           5385.3
14:17:20.450 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:17:20.450 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:17:20.450 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:20 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3181379584
14:17:20.450 WARN  gatk -   MAF Elapsed Time: 3.15556058s
14:17:20.522 INFO  Funcotator - ------------------------------------------------------------
14:17:20.522 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:20.522 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:20.522 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:20.522 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:20.522 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:20 PM UTC
14:17:20.522 INFO  Funcotator - ------------------------------------------------------------
14:17:20.522 INFO  Funcotator - ------------------------------------------------------------
14:17:20.522 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:20.522 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:20.522 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:20.522 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:20.522 INFO  Funcotator - Deflater: IntelDeflater
14:17:20.522 INFO  Funcotator - Inflater: IntelInflater
14:17:20.522 INFO  Funcotator - GCS max retries/reopens: 20
14:17:20.522 INFO  Funcotator - Requester pays: disabled
14:17:20.522 INFO  Funcotator - Initializing engine
14:17:20.524 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
14:17:20.525 INFO  Funcotator - Done initializing engine
14:17:20.525 INFO  Funcotator - Validating sequence dictionaries...
14:17:20.526 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:20.526 INFO  Funcotator - Initializing data sources...
14:17:20.526 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:20.526 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:20.526 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
14:17:20.526 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
14:17:20.526 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
14:17:20.527 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
14:17:20.527 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
14:17:20.527 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
14:17:20.527 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
14:17:20.527 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
14:17:20.527 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
14:17:20.528 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
14:17:20.528 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
14:17:20.528 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
14:17:20.528 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
14:17:20.528 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
14:17:20.528 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
14:17:20.528 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:20.529 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
14:17:20.529 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
14:17:20.573 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
14:17:20.592 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
14:17:20.599 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
14:17:20.599 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
14:17:20.600 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
14:17:20.600 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
14:17:21.189 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
14:17:21.228 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
14:17:21.228 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:21.229 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
14:17:21.229 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
14:17:21.311 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:21.312 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
14:17:21.312 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
14:17:21.340 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
14:17:21.340 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	2025-06-02 14:17:21	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:21.340 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
14:17:21.341 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
14:17:21.341 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
14:17:21.341 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:21.342 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
14:17:21.344 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
14:17:21.346 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
14:17:21.349 INFO  Funcotator - Initializing Funcotator Engine...
14:17:21.349 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:21.349 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.
14:17:21.349 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator1453387921506034419.vcf
14:17:21.351 INFO  ProgressMeter - Starting traversal
14:17:21.351 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:22.495 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:17:22.495 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:17:23.379 INFO  ProgressMeter -             unmapped              0.0                   168           4970.4
14:17:23.379 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:17:23.379 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:17:23.386 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:23 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3181379584
14:17:23.386 WARN  gatk -   VCF Elapsed Time: 2.932830119s
14:17:23.387 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator1453387921506034419.vcf
14:17:23.389 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
14:17:23.455 INFO  Funcotator - ------------------------------------------------------------
14:17:23.455 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:23.455 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:23.456 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:23.456 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:23.456 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:23 PM UTC
14:17:23.456 INFO  Funcotator - ------------------------------------------------------------
14:17:23.456 INFO  Funcotator - ------------------------------------------------------------
14:17:23.456 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:23.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:23.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:23.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:23.456 INFO  Funcotator - Deflater: IntelDeflater
14:17:23.456 INFO  Funcotator - Inflater: IntelInflater
14:17:23.456 INFO  Funcotator - GCS max retries/reopens: 20
14:17:23.456 INFO  Funcotator - Requester pays: disabled
14:17:23.456 INFO  Funcotator - Initializing engine
14:17:23.458 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
14:17:23.459 INFO  Funcotator - Done initializing engine
14:17:23.459 INFO  Funcotator - Validating sequence dictionaries...
14:17:23.459 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:23.459 INFO  Funcotator - Initializing data sources...
14:17:23.459 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:23.459 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:23.459 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
14:17:23.460 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
14:17:23.460 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
14:17:23.460 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
14:17:23.460 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
14:17:23.460 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
14:17:23.460 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
14:17:23.461 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
14:17:23.461 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
14:17:23.461 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
14:17:23.461 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
14:17:23.461 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
14:17:23.461 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
14:17:23.461 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
14:17:23.462 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
14:17:23.462 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:23.462 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
14:17:23.462 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
14:17:23.503 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
14:17:23.520 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
14:17:23.527 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
14:17:23.527 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
14:17:23.527 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
14:17:23.528 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
14:17:24.148 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
14:17:24.187 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
14:17:24.187 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:24.188 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
14:17:24.188 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
14:17:24.270 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:24.271 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
14:17:24.271 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
14:17:24.325 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
14:17:24.325 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	2025-06-02 14:17:24	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:24.326 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
14:17:24.326 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
14:17:24.327 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
14:17:24.327 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:24.327 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
14:17:24.329 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
14:17:24.332 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
14:17:24.334 INFO  Funcotator - Initializing Funcotator Engine...
14:17:24.334 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:24.334 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.
14:17:24.334 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator18325241416801089495.maf
14:17:24.334 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
14:17:24.336 INFO  ProgressMeter - Starting traversal
14:17:24.336 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:25.413 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:17:25.413 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:17:26.267 INFO  ProgressMeter -             unmapped              0.0                   168           5220.1
14:17:26.267 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:17:26.267 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:17:26.268 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:26 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3208642560
14:17:26.268 WARN  gatk -   MAF Elapsed Time: 2.876100822s
14:17:26.336 INFO  Funcotator - ------------------------------------------------------------
14:17:26.336 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:26.336 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:26.336 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:26.336 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:26.336 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:26 PM UTC
14:17:26.336 INFO  Funcotator - ------------------------------------------------------------
14:17:26.336 INFO  Funcotator - ------------------------------------------------------------
14:17:26.336 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:26.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:26.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:26.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:26.336 INFO  Funcotator - Deflater: IntelDeflater
14:17:26.336 INFO  Funcotator - Inflater: IntelInflater
14:17:26.336 INFO  Funcotator - GCS max retries/reopens: 20
14:17:26.336 INFO  Funcotator - Requester pays: disabled
14:17:26.336 INFO  Funcotator - Initializing engine
14:17:26.339 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
14:17:26.340 INFO  Funcotator - Done initializing engine
14:17:26.340 INFO  Funcotator - Validating sequence dictionaries...
14:17:26.340 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:26.340 INFO  Funcotator - Initializing data sources...
14:17:26.340 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:26.340 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:26.341 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
14:17:26.341 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
14:17:26.341 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
14:17:26.341 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
14:17:26.341 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
14:17:26.341 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
14:17:26.342 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
14:17:26.342 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
14:17:26.342 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
14:17:26.342 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
14:17:26.342 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
14:17:26.342 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
14:17:26.342 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
14:17:26.343 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
14:17:26.343 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
14:17:26.343 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:26.343 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
14:17:26.343 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
14:17:26.385 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
14:17:26.404 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
14:17:26.411 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
14:17:26.411 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
14:17:26.411 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
14:17:26.412 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
14:17:27.023 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
14:17:27.063 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
14:17:27.063 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:27.064 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
14:17:27.065 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
14:17:27.164 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:27.164 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
14:17:27.165 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
14:17:27.192 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
14:17:27.192 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	2025-06-02 14:17:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:27.193 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
14:17:27.193 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
14:17:27.193 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
14:17:27.193 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:27.194 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
14:17:27.196 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
14:17:27.199 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
14:17:27.201 INFO  Funcotator - Initializing Funcotator Engine...
14:17:27.201 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:27.201 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.
14:17:27.201 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator9628902662390386762.vcf
14:17:27.202 INFO  ProgressMeter - Starting traversal
14:17:27.202 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:27.213 INFO  ProgressMeter -             unmapped              0.0                     1           5454.5
14:17:27.213 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:17:27.213 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:27.215 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:27 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3208642560
14:17:27.215 WARN  gatk -   VCF Elapsed Time: 0.945075423s
14:17:27.215 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator9628902662390386762.vcf
14:17:27.217 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
14:17:27.285 INFO  Funcotator - ------------------------------------------------------------
14:17:27.285 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:27.285 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:27.285 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:27.285 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:27.285 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:27 PM UTC
14:17:27.285 INFO  Funcotator - ------------------------------------------------------------
14:17:27.285 INFO  Funcotator - ------------------------------------------------------------
14:17:27.285 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:27.285 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:27.285 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:27.285 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:27.285 INFO  Funcotator - Deflater: IntelDeflater
14:17:27.285 INFO  Funcotator - Inflater: IntelInflater
14:17:27.285 INFO  Funcotator - GCS max retries/reopens: 20
14:17:27.285 INFO  Funcotator - Requester pays: disabled
14:17:27.285 INFO  Funcotator - Initializing engine
14:17:27.287 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
14:17:27.288 INFO  Funcotator - Done initializing engine
14:17:27.288 INFO  Funcotator - Validating sequence dictionaries...
14:17:27.288 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:27.288 INFO  Funcotator - Initializing data sources...
14:17:27.288 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:27.288 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:27.288 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
14:17:27.289 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
14:17:27.289 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
14:17:27.289 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
14:17:27.289 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
14:17:27.289 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
14:17:27.289 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
14:17:27.289 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
14:17:27.290 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
14:17:27.290 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
14:17:27.290 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
14:17:27.290 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
14:17:27.290 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
14:17:27.290 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
14:17:27.290 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
14:17:27.291 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:27.291 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
14:17:27.291 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
14:17:27.332 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
14:17:27.351 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
14:17:27.358 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
14:17:27.358 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
14:17:27.358 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
14:17:27.359 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
14:17:28.105 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
14:17:28.145 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
14:17:28.146 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:28.146 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
14:17:28.147 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
14:17:28.230 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:28.231 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
14:17:28.231 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
14:17:28.258 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
14:17:28.258 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	2025-06-02 14:17:28	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:28.259 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
14:17:28.259 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
14:17:28.260 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
14:17:28.260 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:28.261 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
14:17:28.262 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
14:17:28.265 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
14:17:28.267 INFO  Funcotator - Initializing Funcotator Engine...
14:17:28.267 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:28.267 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.
14:17:28.267 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator1304735140020135274.maf
14:17:28.268 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
14:17:28.268 INFO  ProgressMeter - Starting traversal
14:17:28.268 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:28.279 INFO  ProgressMeter -             unmapped              0.0                     1           5454.5
14:17:28.279 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:17:28.280 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:28.280 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3288334336
14:17:28.280 WARN  gatk -   MAF Elapsed Time: 1.06268634s
14:17:28.353 INFO  Funcotator - ------------------------------------------------------------
14:17:28.353 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:28.353 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:28.353 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:28.353 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:28.353 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:28 PM UTC
14:17:28.353 INFO  Funcotator - ------------------------------------------------------------
14:17:28.353 INFO  Funcotator - ------------------------------------------------------------
14:17:28.353 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:28.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:28.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:28.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:28.353 INFO  Funcotator - Deflater: IntelDeflater
14:17:28.353 INFO  Funcotator - Inflater: IntelInflater
14:17:28.353 INFO  Funcotator - GCS max retries/reopens: 20
14:17:28.353 INFO  Funcotator - Requester pays: disabled
14:17:28.353 INFO  Funcotator - Initializing engine
14:17:28.380 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
14:17:28.403 INFO  Funcotator - Done initializing engine
14:17:28.403 INFO  Funcotator - Validating sequence dictionaries...
14:17:28.411 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:28.411 INFO  Funcotator - Initializing data sources...
14:17:28.411 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:28.411 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:28.411 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
14:17:28.411 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
14:17:28.411 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
14:17:28.412 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
14:17:28.412 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
14:17:28.412 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
14:17:28.412 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
14:17:28.412 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
14:17:28.413 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
14:17:28.413 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
14:17:28.413 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
14:17:28.413 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
14:17:28.413 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
14:17:28.413 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:28.414 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
14:17:28.456 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/hg38/simple_uniprot_Dec012014.tsv
14:17:28.474 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/hg38/cosmic_tissue.tsv
14:17:28.481 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
14:17:28.481 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
14:17:28.481 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
14:17:28.482 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
14:17:29.150 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
14:17:29.217 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
14:17:29.218 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:29.218 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
14:17:29.219 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
14:17:29.220 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
14:17:29.220 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
14:17:29.221 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
14:17:29.221 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:29.221 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
14:17:29.222 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
14:17:29.224 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
14:17:29.226 INFO  Funcotator - Initializing Funcotator Engine...
14:17:29.230 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:29.230 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator3536871423653217451.vcf
14:17:29.243 INFO  ProgressMeter - Starting traversal
14:17:29.243 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:29.268 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.
14:17:29.270 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:17:29.273 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:29.276 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:29.276 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:29.276 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:29.276 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:29.276 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:29.277 INFO  ProgressMeter -             unmapped              0.0                     5           8823.5
14:17:29.278 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:17:29.278 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:29.289 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3288334336
14:17:29.289 WARN  gatk -   VCF Elapsed Time: 1.008432334s
14:17:29.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator3536871423653217451.vcf
14:17:29.300 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
14:17:29.378 INFO  Funcotator - ------------------------------------------------------------
14:17:29.378 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:29.378 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:29.378 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:29.378 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:29.378 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:29 PM UTC
14:17:29.378 INFO  Funcotator - ------------------------------------------------------------
14:17:29.378 INFO  Funcotator - ------------------------------------------------------------
14:17:29.378 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:29.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:29.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:29.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:29.378 INFO  Funcotator - Deflater: IntelDeflater
14:17:29.378 INFO  Funcotator - Inflater: IntelInflater
14:17:29.378 INFO  Funcotator - GCS max retries/reopens: 20
14:17:29.378 INFO  Funcotator - Requester pays: disabled
14:17:29.378 INFO  Funcotator - Initializing engine
14:17:29.403 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
14:17:29.426 INFO  Funcotator - Done initializing engine
14:17:29.426 INFO  Funcotator - Validating sequence dictionaries...
14:17:29.434 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:29.434 INFO  Funcotator - Initializing data sources...
14:17:29.434 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:29.434 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:29.434 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
14:17:29.434 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
14:17:29.435 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
14:17:29.435 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
14:17:29.435 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
14:17:29.435 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
14:17:29.435 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
14:17:29.435 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
14:17:29.436 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
14:17:29.436 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
14:17:29.436 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
14:17:29.436 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
14:17:29.436 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
14:17:29.436 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:29.436 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
14:17:29.479 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
14:17:29.498 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
14:17:29.504 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/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:17:29.505 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
14:17:29.505 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
14:17:29.505 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
14:17:30.116 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
14:17:30.182 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
14:17:30.182 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:30.183 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
14:17:30.183 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
14:17:30.184 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
14:17:30.184 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/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:17:30.185 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
14:17:30.185 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:30.185 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
14:17:30.187 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
14:17:30.188 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
14:17:30.190 INFO  Funcotator - Initializing Funcotator Engine...
14:17:30.193 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:30.193 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator6243319341022266287.maf
14:17:30.195 INFO  ProgressMeter - Starting traversal
14:17:30.195 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:30.220 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.
14:17:30.221 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:17:30.222 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:30.226 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:30.226 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:17:30.226 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:30.226 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:30.226 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:17:30.227 INFO  ProgressMeter -             unmapped              0.0                     5           9375.0
14:17:30.227 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:17:30.227 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:30.227 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:30 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3288334336
14:17:30.228 WARN  gatk -   MAF Elapsed Time: 0.919375641s
14:17:30.297 INFO  Funcotator - ------------------------------------------------------------
14:17:30.297 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:30.297 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:30.297 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:30.297 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:30.297 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:30 PM UTC
14:17:30.297 INFO  Funcotator - ------------------------------------------------------------
14:17:30.297 INFO  Funcotator - ------------------------------------------------------------
14:17:30.297 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:30.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:30.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:30.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:30.297 INFO  Funcotator - Deflater: IntelDeflater
14:17:30.297 INFO  Funcotator - Inflater: IntelInflater
14:17:30.297 INFO  Funcotator - GCS max retries/reopens: 20
14:17:30.297 INFO  Funcotator - Requester pays: disabled
14:17:30.297 INFO  Funcotator - Initializing engine
14:17:30.300 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
14:17:30.302 INFO  Funcotator - Done initializing engine
14:17:30.302 INFO  Funcotator - Validating sequence dictionaries...
14:17:30.302 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:30.302 INFO  Funcotator - Initializing data sources...
14:17:30.302 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:30.302 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:30.302 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
14:17:30.302 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
14:17:30.303 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
14:17:30.303 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
14:17:30.303 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
14:17:30.303 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
14:17:30.303 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
14:17:30.304 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
14:17:30.304 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
14:17:30.304 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
14:17:30.304 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
14:17:30.304 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
14:17:30.305 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
14:17:30.305 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
14:17:30.305 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
14:17:30.305 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:30.305 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
14:17:30.305 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
14:17:30.347 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
14:17:30.365 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
14:17:30.372 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
14:17:30.372 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
14:17:30.372 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
14:17:30.373 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
14:17:30.974 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
14:17:31.014 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
14:17:31.014 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:31.014 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
14:17:31.015 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
14:17:31.097 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:31.098 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
14:17:31.098 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
14:17:31.125 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
14:17:31.125 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	2025-06-02 14:17:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:31.126 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
14:17:31.126 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
14:17:31.127 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
14:17:31.127 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:31.127 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
14:17:31.129 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
14:17:31.132 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
14:17:31.134 INFO  Funcotator - Initializing Funcotator Engine...
14:17:31.134 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:31.134 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.
14:17:31.134 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator5074226248747231175.vcf
14:17:31.138 INFO  ProgressMeter - Starting traversal
14:17:31.138 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:37.021 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:17:37.021 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:17:37.023 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          15364.5
14:17:37.023 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:17:37.023 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:17:37.045 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3288334336
14:17:37.045 WARN  gatk -   VCF Elapsed Time: 6.815597415s
14:17:37.046 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator5074226248747231175.vcf
14:17:37.055 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
14:17:37.143 INFO  Funcotator - ------------------------------------------------------------
14:17:37.143 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:37.143 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:37.143 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:37.143 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:37.143 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:37 PM UTC
14:17:37.143 INFO  Funcotator - ------------------------------------------------------------
14:17:37.143 INFO  Funcotator - ------------------------------------------------------------
14:17:37.143 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:37.143 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:37.143 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:37.143 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:37.143 INFO  Funcotator - Deflater: IntelDeflater
14:17:37.143 INFO  Funcotator - Inflater: IntelInflater
14:17:37.143 INFO  Funcotator - GCS max retries/reopens: 20
14:17:37.143 INFO  Funcotator - Requester pays: disabled
14:17:37.143 INFO  Funcotator - Initializing engine
14:17:37.146 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
14:17:37.147 INFO  Funcotator - Done initializing engine
14:17:37.147 INFO  Funcotator - Validating sequence dictionaries...
14:17:37.147 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:37.147 INFO  Funcotator - Initializing data sources...
14:17:37.147 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:37.147 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:37.147 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
14:17:37.147 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
14:17:37.148 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
14:17:37.148 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
14:17:37.148 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
14:17:37.148 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
14:17:37.148 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
14:17:37.148 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
14:17:37.148 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
14:17:37.149 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
14:17:37.149 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
14:17:37.149 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
14:17:37.149 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
14:17:37.149 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
14:17:37.149 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
14:17:37.149 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:37.149 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
14:17:37.150 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
14:17:37.191 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
14:17:37.208 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
14:17:37.215 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
14:17:37.215 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
14:17:37.215 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
14:17:37.216 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
14:17:37.817 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
14:17:37.856 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
14:17:37.856 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:37.857 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
14:17:37.857 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
14:17:37.939 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:37.939 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
14:17:37.940 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
14:17:37.967 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
14:17:37.967 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	2025-06-02 14:17:37	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:37.967 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
14:17:37.968 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
14:17:37.969 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
14:17:37.969 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:37.969 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
14:17:37.971 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
14:17:37.973 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
14:17:37.975 INFO  Funcotator - Initializing Funcotator Engine...
14:17:37.976 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:37.976 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.
14:17:37.976 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator12772581890230500077.maf
14:17:37.976 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
14:17:37.976 INFO  ProgressMeter - Starting traversal
14:17:37.976 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:43.444 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:17:43.445 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:17:43.446 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16530.2
14:17:43.446 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:17:43.446 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:17:43.447 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3288334336
14:17:43.447 WARN  gatk -   MAF Elapsed Time: 6.372301372s
14:17:43.529 INFO  Funcotator - ------------------------------------------------------------
14:17:43.530 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:43.530 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:43.530 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:43.530 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:43.530 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:43 PM UTC
14:17:43.530 INFO  Funcotator - ------------------------------------------------------------
14:17:43.530 INFO  Funcotator - ------------------------------------------------------------
14:17:43.530 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:43.530 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:43.530 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:43.530 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:43.530 INFO  Funcotator - Deflater: IntelDeflater
14:17:43.530 INFO  Funcotator - Inflater: IntelInflater
14:17:43.530 INFO  Funcotator - GCS max retries/reopens: 20
14:17:43.530 INFO  Funcotator - Requester pays: disabled
14:17:43.530 INFO  Funcotator - Initializing engine
14:17:43.532 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
14:17:43.533 INFO  Funcotator - Done initializing engine
14:17:43.533 INFO  Funcotator - Validating sequence dictionaries...
14:17:43.533 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:43.533 INFO  Funcotator - Initializing data sources...
14:17:43.533 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:43.533 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:43.534 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
14:17:43.534 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
14:17:43.534 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
14:17:43.534 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
14:17:43.534 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
14:17:43.535 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
14:17:43.535 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
14:17:43.535 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
14:17:43.535 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
14:17:43.535 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
14:17:43.535 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
14:17:43.535 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
14:17:43.536 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
14:17:43.536 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
14:17:43.536 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
14:17:43.536 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:43.536 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
14:17:43.536 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
14:17:43.578 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
14:17:43.595 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
14:17:43.602 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
14:17:43.602 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
14:17:43.602 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
14:17:43.603 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
14:17:44.193 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
14:17:44.232 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
14:17:44.232 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:44.233 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
14:17:44.233 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
14:17:44.315 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:44.316 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
14:17:44.316 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
14:17:44.343 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
14:17:44.343 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	2025-06-02 14:17:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:44.344 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
14:17:44.344 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
14:17:44.345 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
14:17:44.345 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:44.345 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
14:17:44.347 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
14:17:44.349 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
14:17:44.351 INFO  Funcotator - Initializing Funcotator Engine...
14:17:44.352 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:44.352 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.
14:17:44.352 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator15474242679703681727.vcf
14:17:44.353 INFO  ProgressMeter - Starting traversal
14:17:44.353 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:46.581 INFO  ProgressMeter -             unmapped              0.0                   198           5332.1
14:17:46.581 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:17:46.581 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:17:46.590 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:46 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3288334336
14:17:46.660 INFO  Funcotator - ------------------------------------------------------------
14:17:46.660 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:46.660 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:46.660 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:46.660 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:46.660 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:46 PM UTC
14:17:46.660 INFO  Funcotator - ------------------------------------------------------------
14:17:46.660 INFO  Funcotator - ------------------------------------------------------------
14:17:46.660 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:46.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:46.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:46.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:46.661 INFO  Funcotator - Deflater: IntelDeflater
14:17:46.661 INFO  Funcotator - Inflater: IntelInflater
14:17:46.661 INFO  Funcotator - GCS max retries/reopens: 20
14:17:46.661 INFO  Funcotator - Requester pays: disabled
14:17:46.661 INFO  Funcotator - Initializing engine
14:17:46.663 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
14:17:46.664 INFO  Funcotator - Done initializing engine
14:17:46.664 INFO  Funcotator - Validating sequence dictionaries...
14:17:46.664 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:46.664 INFO  Funcotator - Initializing data sources...
14:17:46.664 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:46.664 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:46.664 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
14:17:46.664 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
14:17:46.665 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
14:17:46.665 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
14:17:46.665 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
14:17:46.665 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
14:17:46.665 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
14:17:46.665 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 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
14:17:46.666 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:46.666 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
14:17:46.667 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
14:17:46.708 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
14:17:46.726 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
14:17:46.733 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
14:17:46.733 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
14:17:46.734 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
14:17:46.734 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
14:17:47.372 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
14:17:47.412 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
14:17:47.413 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:47.413 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
14:17:47.414 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
14:17:47.496 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:47.496 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
14:17:47.497 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
14:17:47.524 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
14:17:47.524 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	2025-06-02 14:17:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:47.525 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
14:17:47.525 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
14:17:47.526 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
14:17:47.526 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:47.526 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
14:17:47.528 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
14:17:47.531 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
14:17:47.533 INFO  Funcotator - Initializing Funcotator Engine...
14:17:47.533 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:47.533 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.
14:17:47.533 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator215608356100485958.maf
14:17:47.533 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
14:17:47.533 INFO  ProgressMeter - Starting traversal
14:17:47.533 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:49.689 INFO  ProgressMeter -             unmapped              0.0                   198           5510.2
14:17:49.689 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:17:49.689 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:17:49.689 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3288334336
14:17:49.763 INFO  Funcotator - ------------------------------------------------------------
14:17:49.763 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:49.763 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:49.763 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:49.763 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:49.763 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:49 PM UTC
14:17:49.763 INFO  Funcotator - ------------------------------------------------------------
14:17:49.763 INFO  Funcotator - ------------------------------------------------------------
14:17:49.763 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:49.763 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:49.763 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:49.763 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:49.763 INFO  Funcotator - Deflater: IntelDeflater
14:17:49.763 INFO  Funcotator - Inflater: IntelInflater
14:17:49.763 INFO  Funcotator - GCS max retries/reopens: 20
14:17:49.763 INFO  Funcotator - Requester pays: disabled
14:17:49.763 INFO  Funcotator - Initializing engine
14:17:49.765 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
14:17:49.766 INFO  Funcotator - Done initializing engine
14:17:49.767 INFO  Funcotator - Validating sequence dictionaries...
14:17:49.767 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:49.767 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3288334336
14:17:49.839 INFO  Funcotator - ------------------------------------------------------------
14:17:49.839 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:49.839 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:49.839 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:49.839 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:49.839 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:49 PM UTC
14:17:49.839 INFO  Funcotator - ------------------------------------------------------------
14:17:49.839 INFO  Funcotator - ------------------------------------------------------------
14:17:49.839 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:49.839 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:49.839 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:49.839 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:49.839 INFO  Funcotator - Deflater: IntelDeflater
14:17:49.839 INFO  Funcotator - Inflater: IntelInflater
14:17:49.839 INFO  Funcotator - GCS max retries/reopens: 20
14:17:49.839 INFO  Funcotator - Requester pays: disabled
14:17:49.839 INFO  Funcotator - Initializing engine
14:17:49.841 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
14:17:49.860 INFO  Funcotator - Done initializing engine
14:17:49.860 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:49.860 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:49.860 INFO  Funcotator - Initializing data sources...
14:17:49.860 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:17:49.860 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:49.860 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
14:17:49.860 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
14:17:49.861 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
14:17:49.861 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:49.861 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
14:17:49.861 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:49.861 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
14:17:49.862 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
14:17:49.862 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
14:17:49.862 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:17:49.863 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
14:17:49.870 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
14:17:49.879 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
14:17:49.887 INFO  Funcotator - Initializing Funcotator Engine...
14:17:49.891 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:49.891 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13203213902151675862.vcf
14:17:49.904 INFO  ProgressMeter - Starting traversal
14:17:49.905 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:49.934 INFO  ProgressMeter -             unmapped              0.0                   100         206896.6
14:17:49.934 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:17:49.934 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:17:49.940 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3288334336
14:17:49.941 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13203213902151675862.vcf
14:17:50.021 INFO  Funcotator - ------------------------------------------------------------
14:17:50.021 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:50.021 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:50.021 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:50.021 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:50.021 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:50 PM UTC
14:17:50.021 INFO  Funcotator - ------------------------------------------------------------
14:17:50.021 INFO  Funcotator - ------------------------------------------------------------
14:17:50.021 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:50.021 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:50.021 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:50.022 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:50.022 INFO  Funcotator - Deflater: IntelDeflater
14:17:50.022 INFO  Funcotator - Inflater: IntelInflater
14:17:50.022 INFO  Funcotator - GCS max retries/reopens: 20
14:17:50.022 INFO  Funcotator - Requester pays: disabled
14:17:50.022 INFO  Funcotator - Initializing engine
14:17:50.023 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
14:17:50.024 INFO  Funcotator - Done initializing engine
14:17:50.024 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:50.024 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:50.024 INFO  Funcotator - Initializing data sources...
14:17:50.024 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:17:50.024 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:50.025 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
14:17:50.025 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
14:17:50.025 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
14:17:50.025 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:50.025 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
14:17:50.025 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:50.026 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
14:17:50.026 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
14:17:50.026 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
14:17:50.026 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:17:50.027 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
14:17:50.028 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
14:17:50.029 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
14:17:50.029 INFO  Funcotator - Initializing Funcotator Engine...
14:17:50.029 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:17:50.030 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.
14:17:50.030 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9643708686715987548.vcf
14:17:50.037 INFO  ProgressMeter - Starting traversal
14:17:50.038 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:50.046 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
14:17:50.047 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:17:50.047 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:17:50.049 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3288334336
14:17:50.050 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9643708686715987548.vcf
14:17:50.122 INFO  Funcotator - ------------------------------------------------------------
14:17:50.122 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:50.122 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:50.122 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:50.122 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:50.122 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:50 PM UTC
14:17:50.122 INFO  Funcotator - ------------------------------------------------------------
14:17:50.122 INFO  Funcotator - ------------------------------------------------------------
14:17:50.122 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:50.122 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:50.122 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:50.122 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:50.122 INFO  Funcotator - Deflater: IntelDeflater
14:17:50.122 INFO  Funcotator - Inflater: IntelInflater
14:17:50.122 INFO  Funcotator - GCS max retries/reopens: 20
14:17:50.122 INFO  Funcotator - Requester pays: disabled
14:17:50.122 INFO  Funcotator - Initializing engine
14:17:50.123 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
14:17:50.135 INFO  Funcotator - Done initializing engine
14:17:50.135 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:50.135 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:50.135 INFO  Funcotator - Initializing data sources...
14:17:50.135 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:17:50.135 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:50.135 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
14:17:50.135 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
14:17:50.136 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
14:17:50.136 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:50.136 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
14:17:50.136 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:50.136 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
14:17:50.137 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
14:17:50.137 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
14:17:50.137 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:17:50.138 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
14:17:50.146 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
14:17:50.154 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
14:17:50.162 INFO  Funcotator - Initializing Funcotator Engine...
14:17:50.167 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:50.167 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12738225096903755867.vcf
14:17:50.178 INFO  ProgressMeter - Starting traversal
14:17:50.178 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:50.182 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)
14:17:50.183 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)
14:17:50.183 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.183 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:17:50.183 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:17:50.183 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:17:50.185 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.185 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:17:50.186 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:17:50.186 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:17:50.186 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)
14:17:50.187 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)
14:17:50.187 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.187 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:17:50.187 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:17:50.187 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:17:50.187 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)
14:17:50.188 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)
14:17:50.188 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:17:50.188 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:17:50.188 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:17:50.188 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:17:50.189 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.189 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:17:50.189 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:17:50.189 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:17:50.190 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.190 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:17:50.190 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:17:50.190 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:17:50.191 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)
14:17:50.191 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)
14:17:50.191 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:17:50.191 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:17:50.191 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:17:50.191 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:17:50.192 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)
14:17:50.192 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)
14:17:50.192 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.192 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:17:50.192 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:17:50.192 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:17:50.193 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:17:50.193 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:17:50.194 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:17:50.194 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:17:50.194 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)
14:17:50.194 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)
14:17:50.194 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:17:50.195 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:17:50.195 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:17:50.195 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:17:50.195 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
14:17:50.195 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:17:50.195 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:17:50.200 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3288334336
14:17:50.201 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12738225096903755867.vcf
14:17:50.283 INFO  Funcotator - ------------------------------------------------------------
14:17:50.283 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:50.283 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:50.283 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:50.283 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:50.283 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:50 PM UTC
14:17:50.283 INFO  Funcotator - ------------------------------------------------------------
14:17:50.283 INFO  Funcotator - ------------------------------------------------------------
14:17:50.283 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:50.283 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:50.283 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:50.283 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:50.283 INFO  Funcotator - Deflater: IntelDeflater
14:17:50.283 INFO  Funcotator - Inflater: IntelInflater
14:17:50.283 INFO  Funcotator - GCS max retries/reopens: 20
14:17:50.283 INFO  Funcotator - Requester pays: disabled
14:17:50.283 INFO  Funcotator - Initializing engine
14:17:50.285 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
14:17:50.287 INFO  Funcotator - Done initializing engine
14:17:50.287 INFO  Funcotator - Validating sequence dictionaries...
14:17:50.287 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:50.287 INFO  Funcotator - Initializing data sources...
14:17:50.287 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:50.287 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:50.287 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
14:17:50.287 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
14:17:50.287 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
14:17:50.288 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
14:17:50.288 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
14:17:50.288 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
14:17:50.288 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
14:17:50.288 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
14:17:50.288 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
14:17:50.289 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
14:17:50.289 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
14:17:50.289 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
14:17:50.289 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
14:17:50.289 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
14:17:50.289 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
14:17:50.289 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:50.290 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
14:17:50.290 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
14:17:50.339 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
14:17:50.357 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
14:17:50.364 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
14:17:50.364 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
14:17:50.364 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
14:17:50.365 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
14:17:50.986 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
14:17:51.025 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
14:17:51.026 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:51.026 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
14:17:51.027 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
14:17:51.110 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:51.110 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
14:17:51.111 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
14:17:51.138 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
14:17:51.138 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	2025-06-02 14:17:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:51.139 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
14:17:51.139 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
14:17:51.140 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
14:17:51.140 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:51.140 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
14:17:51.142 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
14:17:51.145 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
14:17:51.147 INFO  Funcotator - Initializing Funcotator Engine...
14:17:51.147 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:51.147 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.
14:17:51.147 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator950638687209770108.vcf
14:17:51.152 INFO  ProgressMeter - Starting traversal
14:17:51.152 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:51.208 INFO  ProgressMeter -             unmapped              0.0                     1           1071.4
14:17:51.208 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:17:51.208 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:51.209 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3288334336
14:17:51.209 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator950638687209770108.vcf
14:17:51.280 INFO  Funcotator - ------------------------------------------------------------
14:17:51.280 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:51.280 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:51.280 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:51.280 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:51.280 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:51 PM UTC
14:17:51.280 INFO  Funcotator - ------------------------------------------------------------
14:17:51.280 INFO  Funcotator - ------------------------------------------------------------
14:17:51.280 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:51.280 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:51.280 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:51.280 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:51.280 INFO  Funcotator - Deflater: IntelDeflater
14:17:51.280 INFO  Funcotator - Inflater: IntelInflater
14:17:51.280 INFO  Funcotator - GCS max retries/reopens: 20
14:17:51.280 INFO  Funcotator - Requester pays: disabled
14:17:51.280 INFO  Funcotator - Initializing engine
14:17:51.282 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
14:17:51.283 INFO  Funcotator - Done initializing engine
14:17:51.283 INFO  Funcotator - Validating sequence dictionaries...
14:17:51.284 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:51.284 INFO  Funcotator - Initializing data sources...
14:17:51.284 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:51.284 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:51.284 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
14:17:51.284 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
14:17:51.284 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
14:17:51.284 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
14:17:51.285 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
14:17:51.285 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
14:17:51.285 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
14:17:51.285 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
14:17:51.285 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
14:17:51.285 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
14:17:51.285 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
14:17:51.286 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
14:17:51.286 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
14:17:51.286 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
14:17:51.286 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
14:17:51.286 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:51.286 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
14:17:51.287 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
14:17:51.329 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
14:17:51.347 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
14:17:51.354 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
14:17:51.354 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
14:17:51.354 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
14:17:51.355 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
14:17:52.099 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
14:17:52.140 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
14:17:52.141 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:52.141 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
14:17:52.142 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
14:17:52.226 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:52.226 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:17:52.227 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
14:17:52.255 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
14:17:52.255 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	2025-06-02 14:17:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:52.256 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
14:17:52.256 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
14:17:52.257 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
14:17:52.257 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:52.257 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
14:17:52.259 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
14:17:52.262 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
14:17:52.264 INFO  Funcotator - Initializing Funcotator Engine...
14:17:52.264 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:17:52.264 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.
14:17:52.264 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator17770983222889279295.vcf
14:17:52.268 INFO  ProgressMeter - Starting traversal
14:17:52.268 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:52.274 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.326 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:17:52.330 INFO  ProgressMeter -             unmapped              0.0                     2           1935.5
14:17:52.330 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:17:52.330 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:52.331 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:52.332 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator17770983222889279295.vcf
14:17:52.403 INFO  Funcotator - ------------------------------------------------------------
14:17:52.403 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:52.403 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:52.403 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:52.403 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:52.403 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:52 PM UTC
14:17:52.403 INFO  Funcotator - ------------------------------------------------------------
14:17:52.403 INFO  Funcotator - ------------------------------------------------------------
14:17:52.403 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:52.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:52.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:52.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:52.403 INFO  Funcotator - Deflater: IntelDeflater
14:17:52.403 INFO  Funcotator - Inflater: IntelInflater
14:17:52.403 INFO  Funcotator - GCS max retries/reopens: 20
14:17:52.403 INFO  Funcotator - Requester pays: disabled
14:17:52.403 INFO  Funcotator - Initializing engine
14:17:52.405 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
14:17:52.406 INFO  Funcotator - Done initializing engine
14:17:52.406 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:52.407 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:52.407 INFO  Funcotator - Initializing data sources...
14:17:52.407 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:52.407 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:52.407 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
14:17:52.407 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
14:17:52.407 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
14:17:52.407 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
14:17:52.408 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
14:17:52.408 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
14:17:52.408 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
14:17:52.408 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
14:17:52.408 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
14:17:52.409 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
14:17:52.409 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
14:17:52.409 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
14:17:52.409 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
14:17:52.409 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
14:17:52.409 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
14:17:52.409 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:52.409 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
14:17:52.410 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
14:17:52.453 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
14:17:52.471 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
14:17:52.477 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
14:17:52.478 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
14:17:52.478 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
14:17:52.478 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
14:17:53.036 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
14:17:53.075 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
14:17:53.075 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:53.076 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
14:17:53.076 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
14:17:53.294 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:53.294 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
14:17:53.294 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
14:17:53.322 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
14:17:53.322 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	2025-06-02 14:17:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:53.323 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
14:17:53.323 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
14:17:53.324 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
14:17:53.324 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:53.325 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
14:17:53.326 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
14:17:53.329 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
14:17:53.331 INFO  Funcotator - Initializing Funcotator Engine...
14:17:53.331 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:17:53.331 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.
14:17:53.331 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
14:17:53.331 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
14:17:53.331 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
14:17:53.331 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2142916887770092946.vcf
14:17:53.335 INFO  ProgressMeter - Starting traversal
14:17:53.335 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:53.373 INFO  ProgressMeter -             unmapped              0.0                     1           1578.9
14:17:53.373 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:17:53.373 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:53.374 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:53.375 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2142916887770092946.vcf
14:17:53.376 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
[June 2, 2025 at 2:17:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3334471680
[June 2, 2025 at 2:17:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3334471680
14:17:53.629 INFO  Funcotator - ------------------------------------------------------------
14:17:53.629 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:53.629 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:53.629 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:53.629 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:53.629 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:53 PM UTC
14:17:53.629 INFO  Funcotator - ------------------------------------------------------------
14:17:53.629 INFO  Funcotator - ------------------------------------------------------------
14:17:53.629 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:53.629 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:53.629 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:53.629 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:53.629 INFO  Funcotator - Deflater: IntelDeflater
14:17:53.629 INFO  Funcotator - Inflater: IntelInflater
14:17:53.629 INFO  Funcotator - GCS max retries/reopens: 20
14:17:53.629 INFO  Funcotator - Requester pays: disabled
14:17:53.629 INFO  Funcotator - Initializing engine
14:17:53.630 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
14:17:53.645 INFO  Funcotator - Done initializing engine
14:17:53.645 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:53.645 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:53.645 INFO  Funcotator - Initializing data sources...
14:17:53.645 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:17:53.645 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:53.645 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
14:17:53.645 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
14:17:53.646 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
14:17:53.646 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:53.646 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
14:17:53.646 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:53.646 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
14:17:53.647 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
14:17:53.647 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
14:17:53.647 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:17:53.648 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
14:17:53.655 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
14:17:53.664 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
14:17:53.672 INFO  Funcotator - Initializing Funcotator Engine...
14:17:53.679 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:53.679 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3452268923629745871.vcf
14:17:53.691 INFO  ProgressMeter - Starting traversal
14:17:53.691 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:53.718 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
14:17:53.718 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:17:53.718 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:17:53.723 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3334471680
14:17:53.724 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3452268923629745871.vcf
14:17:53.805 INFO  Funcotator - ------------------------------------------------------------
14:17:53.805 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:53.806 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:53.806 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:53.806 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:53.806 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:53 PM UTC
14:17:53.806 INFO  Funcotator - ------------------------------------------------------------
14:17:53.806 INFO  Funcotator - ------------------------------------------------------------
14:17:53.806 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:53.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:53.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:53.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:53.806 INFO  Funcotator - Deflater: IntelDeflater
14:17:53.806 INFO  Funcotator - Inflater: IntelInflater
14:17:53.806 INFO  Funcotator - GCS max retries/reopens: 20
14:17:53.806 INFO  Funcotator - Requester pays: disabled
14:17:53.806 INFO  Funcotator - Initializing engine
14:17:53.808 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
14:17:53.809 INFO  Funcotator - Done initializing engine
14:17:53.809 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:53.809 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:53.809 INFO  Funcotator - Initializing data sources...
14:17:53.809 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/
14:17:53.809 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:53.810 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
14:17:53.810 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
14:17:53.810 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
14:17:53.810 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:53.810 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
14:17:53.810 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:53.810 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
14:17:53.811 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
14:17:53.811 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
14:17:53.811 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:17:53.812 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
14:17:53.814 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
14:17:53.816 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
14:17:53.818 INFO  Funcotator - Initializing Funcotator Engine...
14:17:53.818 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:17:53.818 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.
14:17:53.818 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:53.819 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing8334093896331577520.vcf
14:17:53.821 INFO  ProgressMeter - Starting traversal
14:17:53.821 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:53.846 INFO  ProgressMeter -             unmapped              0.0                     1           2400.0
14:17:53.846 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:17:53.846 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
14:17:53.848 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3334471680
14:17:53.849 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing8334093896331577520.vcf
14:17:53.918 INFO  Funcotator - ------------------------------------------------------------
14:17:53.918 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:53.918 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:53.918 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:53.918 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:53.918 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:53 PM UTC
14:17:53.918 INFO  Funcotator - ------------------------------------------------------------
14:17:53.918 INFO  Funcotator - ------------------------------------------------------------
14:17:53.918 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:53.918 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:53.918 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:53.918 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:53.918 INFO  Funcotator - Deflater: IntelDeflater
14:17:53.918 INFO  Funcotator - Inflater: IntelInflater
14:17:53.918 INFO  Funcotator - GCS max retries/reopens: 20
14:17:53.918 INFO  Funcotator - Requester pays: disabled
14:17:53.918 INFO  Funcotator - Initializing engine
14:17:53.919 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
14:17:53.920 INFO  Funcotator - Done initializing engine
14:17:53.920 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:53.920 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:53.920 INFO  Funcotator - Initializing data sources...
14:17:53.920 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:53.920 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:53.920 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
14:17:53.920 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
14:17:53.921 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
14:17:53.921 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
14:17:53.921 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
14:17:53.921 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
14:17:53.921 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
14:17:53.921 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
14:17:53.922 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
14:17:53.922 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
14:17:53.922 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
14:17:53.922 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
14:17:53.922 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
14:17:53.922 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
14:17:53.922 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
14:17:53.923 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:53.923 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
14:17:53.923 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
14:17:53.964 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
14:17:53.982 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
14:17:53.989 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
14:17:53.989 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
14:17:53.989 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
14:17:53.990 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
14:17:54.605 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
14:17:54.644 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
14:17:54.644 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:54.645 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
14:17:54.646 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
14:17:54.728 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:54.728 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
14:17:54.729 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
14:17:54.756 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
14:17:54.757 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	2025-06-02 14:17:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:54.757 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
14:17:54.757 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
14:17:54.758 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
14:17:54.758 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:54.759 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
14:17:54.761 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
14:17:54.763 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
14:17:54.765 INFO  Funcotator - Initializing Funcotator Engine...
14:17:54.765 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
14:17:54.765 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:54.765 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:54.765 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:54.765 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:54.766 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:54.766 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:54.766 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18158574779438591855.vcf
14:17:54.766 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
14:17:54.767 INFO  ProgressMeter - Starting traversal
14:17:54.767 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:54.789 INFO  ProgressMeter -             unmapped              0.0                     3           8181.8
14:17:54.789 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:54.789 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:54.792 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3334471680
14:17:54.860 INFO  Funcotator - ------------------------------------------------------------
14:17:54.860 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:54.860 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:54.860 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:54.860 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:54.860 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:54 PM UTC
14:17:54.860 INFO  Funcotator - ------------------------------------------------------------
14:17:54.860 INFO  Funcotator - ------------------------------------------------------------
14:17:54.860 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:54.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:54.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:54.861 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:54.861 INFO  Funcotator - Deflater: IntelDeflater
14:17:54.861 INFO  Funcotator - Inflater: IntelInflater
14:17:54.861 INFO  Funcotator - GCS max retries/reopens: 20
14:17:54.861 INFO  Funcotator - Requester pays: disabled
14:17:54.861 INFO  Funcotator - Initializing engine
14:17:54.861 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
14:17:54.862 INFO  Funcotator - Done initializing engine
14:17:54.862 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:54.862 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:54.862 INFO  Funcotator - Initializing data sources...
14:17:54.862 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:54.862 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:54.862 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
14:17:54.862 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
14:17:54.863 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
14:17:54.863 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
14:17:54.863 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
14:17:54.863 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
14:17:54.863 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
14:17:54.863 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
14:17:54.864 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
14:17:54.864 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
14:17:54.864 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
14:17:54.864 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
14:17:54.864 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
14:17:54.864 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
14:17:54.865 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
14:17:54.865 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:54.865 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
14:17:54.865 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
14:17:54.906 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
14:17:54.923 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
14:17:54.929 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
14:17:54.930 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
14:17:54.930 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
14:17:54.930 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
14:17:55.540 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
14:17:55.580 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
14:17:55.580 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:55.580 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
14:17:55.581 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
14:17:55.664 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:55.664 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
14:17:55.665 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
14:17:55.692 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
14:17:55.692 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	2025-06-02 14:17:55	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:55.693 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
14:17:55.693 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
14:17:55.693 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
14:17:55.693 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:55.694 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
14:17:55.696 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
14:17:55.700 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
14:17:55.703 INFO  Funcotator - Initializing Funcotator Engine...
14:17:55.703 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:55.703 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:55.704 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18327590342305942827.vcf
14:17:55.705 INFO  ProgressMeter - Starting traversal
14:17:55.705 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:55.826 INFO  ProgressMeter -             unmapped              0.0                     4           1983.5
14:17:55.826 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:55.826 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:55.826 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:55 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:55.896 INFO  Funcotator - ------------------------------------------------------------
14:17:55.896 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:55.896 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:55.896 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:55.896 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:55.896 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:55 PM UTC
14:17:55.896 INFO  Funcotator - ------------------------------------------------------------
14:17:55.896 INFO  Funcotator - ------------------------------------------------------------
14:17:55.896 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:55.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:55.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:55.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:55.896 INFO  Funcotator - Deflater: IntelDeflater
14:17:55.896 INFO  Funcotator - Inflater: IntelInflater
14:17:55.896 INFO  Funcotator - GCS max retries/reopens: 20
14:17:55.896 INFO  Funcotator - Requester pays: disabled
14:17:55.896 INFO  Funcotator - Initializing engine
14:17:55.897 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
14:17:55.898 INFO  Funcotator - Done initializing engine
14:17:55.898 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:55.898 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:55.898 INFO  Funcotator - Initializing data sources...
14:17:55.898 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:55.898 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:55.899 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
14:17:55.899 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
14:17:55.899 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
14:17:55.899 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
14:17:55.899 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
14:17:55.900 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
14:17:55.900 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
14:17:55.900 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
14:17:55.900 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
14:17:55.900 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
14:17:55.900 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
14:17:55.901 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
14:17:55.901 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
14:17:55.901 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
14:17:55.901 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
14:17:55.901 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:55.901 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
14:17:55.902 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
14:17:55.945 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
14:17:55.963 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
14:17:55.971 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
14:17:55.971 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
14:17:55.971 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
14:17:55.972 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
14:17:56.560 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
14:17:56.600 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
14:17:56.600 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:56.601 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
14:17:56.602 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
14:17:56.684 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:56.685 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
14:17:56.685 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
14:17:56.712 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
14:17:56.712 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	2025-06-02 14:17:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:56.713 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
14:17:56.713 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
14:17:56.714 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
14:17:56.714 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:56.714 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
14:17:56.716 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
14:17:56.719 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
14:17:56.721 INFO  Funcotator - Initializing Funcotator Engine...
14:17:56.721 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
14:17:56.721 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:56.721 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:56.721 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:56.721 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:56.722 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:56.722 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:56.722 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18138631265619410824.vcf
14:17:56.722 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
14:17:56.723 INFO  ProgressMeter - Starting traversal
14:17:56.723 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:56.808 INFO  ProgressMeter -             unmapped              0.0                     3           2117.6
14:17:56.808 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:56.808 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:56.811 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:56.879 INFO  Funcotator - ------------------------------------------------------------
14:17:56.879 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:56.879 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:56.879 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:56.879 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:56.879 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:56 PM UTC
14:17:56.879 INFO  Funcotator - ------------------------------------------------------------
14:17:56.879 INFO  Funcotator - ------------------------------------------------------------
14:17:56.879 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:56.879 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:56.879 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:56.879 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:56.879 INFO  Funcotator - Deflater: IntelDeflater
14:17:56.879 INFO  Funcotator - Inflater: IntelInflater
14:17:56.879 INFO  Funcotator - GCS max retries/reopens: 20
14:17:56.879 INFO  Funcotator - Requester pays: disabled
14:17:56.879 INFO  Funcotator - Initializing engine
14:17:56.880 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
14:17:56.881 INFO  Funcotator - Done initializing engine
14:17:56.881 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:56.881 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:56.881 INFO  Funcotator - Initializing data sources...
14:17:56.881 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:56.881 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:56.881 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
14:17:56.881 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
14:17:56.881 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
14:17:56.881 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.882 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
14:17:56.883 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
14:17:56.883 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
14:17:56.883 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:56.883 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
14:17:56.883 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
14:17:56.924 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
14:17:56.943 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
14:17:56.950 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
14:17:56.950 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
14:17:56.950 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
14:17:56.950 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
14:17:57.578 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
14:17:57.617 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
14:17:57.617 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:57.618 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
14:17:57.618 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
14:17:57.701 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:57.701 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
14:17:57.702 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
14:17:57.729 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
14:17:57.729 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	2025-06-02 14:17:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:57.729 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
14:17:57.730 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
14:17:57.730 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
14:17:57.730 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:57.731 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
14:17:57.733 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
14:17:57.736 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
14:17:57.738 INFO  Funcotator - Initializing Funcotator Engine...
14:17:57.738 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:57.738 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:57.738 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5442862904750091820.vcf
14:17:57.739 INFO  ProgressMeter - Starting traversal
14:17:57.739 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:57.857 INFO  ProgressMeter -             unmapped              0.0                     4           2033.9
14:17:57.857 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:57.857 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:57.857 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:57 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:57.929 INFO  Funcotator - ------------------------------------------------------------
14:17:57.929 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:57.929 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:57.929 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:57.929 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:57.929 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:57 PM UTC
14:17:57.929 INFO  Funcotator - ------------------------------------------------------------
14:17:57.929 INFO  Funcotator - ------------------------------------------------------------
14:17:57.929 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:57.929 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:57.929 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:57.929 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:57.929 INFO  Funcotator - Deflater: IntelDeflater
14:17:57.929 INFO  Funcotator - Inflater: IntelInflater
14:17:57.929 INFO  Funcotator - GCS max retries/reopens: 20
14:17:57.929 INFO  Funcotator - Requester pays: disabled
14:17:57.929 INFO  Funcotator - Initializing engine
14:17:57.930 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
14:17:57.930 INFO  Funcotator - Done initializing engine
14:17:57.930 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:57.930 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:57.930 INFO  Funcotator - Initializing data sources...
14:17:57.930 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:57.930 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:57.931 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
14:17:57.931 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
14:17:57.931 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
14:17:57.931 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
14:17:57.931 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
14:17:57.931 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
14:17:57.932 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
14:17:57.932 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
14:17:57.932 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
14:17:57.932 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
14:17:57.932 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
14:17:57.932 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
14:17:57.932 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
14:17:57.933 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
14:17:57.933 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
14:17:57.933 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:57.933 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
14:17:57.933 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
14:17:57.975 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
14:17:57.993 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
14:17:58.001 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
14:17:58.001 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
14:17:58.001 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
14:17:58.001 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
14:17:58.592 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
14:17:58.632 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
14:17:58.632 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:58.633 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
14:17:58.633 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
14:17:58.716 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:58.716 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
14:17:58.717 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
14:17:58.744 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
14:17:58.744 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	2025-06-02 14:17:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:58.745 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
14:17:58.745 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
14:17:58.745 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
14:17:58.745 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:58.746 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
14:17:58.748 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
14:17:58.751 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
14:17:58.753 INFO  Funcotator - Initializing Funcotator Engine...
14:17:58.753 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
14:17:58.753 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:17:58.753 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:17:58.753 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:17:58.753 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:17:58.754 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:17:58.754 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:58.754 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10326304124044032152.maf
14:17:58.754 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
14:17:58.755 INFO  ProgressMeter - Starting traversal
14:17:58.755 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:58.837 INFO  ProgressMeter -             unmapped              0.0                     3           2195.1
14:17:58.837 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:17:58.837 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:17:58.837 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3334471680
14:17:58.907 INFO  Funcotator - ------------------------------------------------------------
14:17:58.907 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:17:58.907 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:17:58.907 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:17:58.907 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:17:58.908 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:17:58 PM UTC
14:17:58.908 INFO  Funcotator - ------------------------------------------------------------
14:17:58.908 INFO  Funcotator - ------------------------------------------------------------
14:17:58.908 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:17:58.908 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:17:58.908 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:17:58.908 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:17:58.908 INFO  Funcotator - Deflater: IntelDeflater
14:17:58.908 INFO  Funcotator - Inflater: IntelInflater
14:17:58.908 INFO  Funcotator - GCS max retries/reopens: 20
14:17:58.908 INFO  Funcotator - Requester pays: disabled
14:17:58.908 INFO  Funcotator - Initializing engine
14:17:58.908 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
14:17:58.909 INFO  Funcotator - Done initializing engine
14:17:58.909 INFO  Funcotator - Skipping sequence dictionary validation.
14:17:58.909 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:17:58.909 INFO  Funcotator - Initializing data sources...
14:17:58.909 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:17:58.909 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:17:58.909 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
14:17:58.909 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
14:17:58.910 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
14:17:58.910 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
14:17:58.910 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
14:17:58.910 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
14:17:58.910 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
14:17:58.910 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
14:17:58.910 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
14:17:58.911 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
14:17:58.911 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
14:17:58.911 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
14:17:58.911 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
14:17:58.911 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
14:17:58.911 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
14:17:58.911 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:17:58.911 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
14:17:58.912 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
14:17:58.954 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
14:17:58.972 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
14:17:58.980 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
14:17:58.980 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
14:17:58.980 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
14:17:58.981 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
14:17:59.658 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
14:17:59.697 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
14:17:59.697 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:17:59.698 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
14:17:59.698 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
14:17:59.780 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:17:59.781 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
14:17:59.781 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
14:17:59.808 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
14:17:59.808 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	2025-06-02 14:17:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:17:59.809 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
14:17:59.809 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
14:17:59.810 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
14:17:59.810 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:17:59.810 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
14:17:59.812 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
14:17:59.815 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
14:17:59.817 INFO  Funcotator - Initializing Funcotator Engine...
14:17:59.817 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:17:59.817 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:17:59.817 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7888665012636893257.maf
14:17:59.817 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
14:17:59.818 INFO  ProgressMeter - Starting traversal
14:17:59.818 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:17:59.934 INFO  ProgressMeter -             unmapped              0.0                     4           2069.0
14:17:59.934 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:17:59.935 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:17:59.935 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:17:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3447717888
14:18:00.006 INFO  Funcotator - ------------------------------------------------------------
14:18:00.006 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:00.006 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:00.006 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:00.006 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:00.007 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:00 PM UTC
14:18:00.007 INFO  Funcotator - ------------------------------------------------------------
14:18:00.007 INFO  Funcotator - ------------------------------------------------------------
14:18:00.007 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:00.007 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:00.007 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:00.007 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:00.007 INFO  Funcotator - Deflater: IntelDeflater
14:18:00.007 INFO  Funcotator - Inflater: IntelInflater
14:18:00.007 INFO  Funcotator - GCS max retries/reopens: 20
14:18:00.007 INFO  Funcotator - Requester pays: disabled
14:18:00.007 INFO  Funcotator - Initializing engine
14:18:00.008 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
14:18:00.008 INFO  Funcotator - Done initializing engine
14:18:00.008 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:00.008 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:00.008 INFO  Funcotator - Initializing data sources...
14:18:00.008 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:00.008 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:00.009 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
14:18:00.009 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
14:18:00.009 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
14:18:00.009 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
14:18:00.009 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
14:18:00.009 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
14:18:00.009 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
14:18:00.010 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
14:18:00.010 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
14:18:00.010 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
14:18:00.010 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
14:18:00.010 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
14:18:00.010 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
14:18:00.010 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
14:18:00.011 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
14:18:00.011 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:00.011 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
14:18:00.011 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
14:18:00.053 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
14:18:00.105 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
14:18:00.111 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
14:18:00.112 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
14:18:00.112 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
14:18:00.112 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
14:18:00.714 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
14:18:00.753 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
14:18:00.753 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:00.754 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
14:18:00.754 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
14:18:00.837 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:00.837 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
14:18:00.837 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
14:18:00.865 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
14:18:00.865 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	2025-06-02 14:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:00.865 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
14:18:00.866 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
14:18:00.866 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
14:18:00.866 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:00.867 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
14:18:00.869 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
14:18:00.872 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
14:18:00.874 INFO  Funcotator - Initializing Funcotator Engine...
14:18:00.874 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
14:18:00.874 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:18:00.874 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:18:00.874 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:18:00.874 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:18:00.875 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:18:00.875 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:00.875 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8294728397825111840.maf
14:18:00.875 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
14:18:00.876 INFO  ProgressMeter - Starting traversal
14:18:00.876 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:00.897 INFO  ProgressMeter -             unmapped              0.0                     3           8571.4
14:18:00.897 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:18:00.897 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:18:00.897 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3447717888
14:18:00.965 INFO  Funcotator - ------------------------------------------------------------
14:18:00.965 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:00.965 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:00.965 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:00.965 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:00.965 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:00 PM UTC
14:18:00.965 INFO  Funcotator - ------------------------------------------------------------
14:18:00.965 INFO  Funcotator - ------------------------------------------------------------
14:18:00.965 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:00.965 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:00.965 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:00.965 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:00.965 INFO  Funcotator - Deflater: IntelDeflater
14:18:00.965 INFO  Funcotator - Inflater: IntelInflater
14:18:00.965 INFO  Funcotator - GCS max retries/reopens: 20
14:18:00.965 INFO  Funcotator - Requester pays: disabled
14:18:00.965 INFO  Funcotator - Initializing engine
14:18:00.966 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
14:18:00.966 INFO  Funcotator - Done initializing engine
14:18:00.966 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:00.966 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:00.966 INFO  Funcotator - Initializing data sources...
14:18:00.966 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:00.967 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:00.967 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
14:18:00.982 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
14:18:00.983 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
14:18:00.983 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
14:18:00.983 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
14:18:00.983 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
14:18:00.983 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
14:18:00.983 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
14:18:00.983 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
14:18:00.984 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
14:18:00.984 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
14:18:00.984 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
14:18:00.984 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
14:18:00.984 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
14:18:00.984 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
14:18:00.984 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:00.984 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
14:18:00.985 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
14:18:01.025 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
14:18:01.043 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
14:18:01.050 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
14:18:01.050 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
14:18:01.050 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
14:18:01.050 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
14:18:01.712 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
14:18:01.752 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
14:18:01.752 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:01.753 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
14:18:01.753 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
14:18:01.836 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:01.836 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
14:18:01.837 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
14:18:01.864 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
14:18:01.864 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	2025-06-02 14:18:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:01.865 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
14:18:01.865 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
14:18:01.865 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
14:18:01.866 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:01.866 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
14:18:01.868 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
14:18:01.871 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
14:18:01.873 INFO  Funcotator - Initializing Funcotator Engine...
14:18:01.873 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:01.873 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:01.873 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5048040560794599013.maf
14:18:01.873 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
14:18:01.873 INFO  ProgressMeter - Starting traversal
14:18:01.873 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:01.990 INFO  ProgressMeter -             unmapped              0.0                     4           2051.3
14:18:01.990 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:18:01.990 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:18:01.990 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3447717888
14:18:02.058 INFO  Funcotator - ------------------------------------------------------------
14:18:02.058 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.058 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.058 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.058 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.058 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.058 INFO  Funcotator - ------------------------------------------------------------
14:18:02.058 INFO  Funcotator - ------------------------------------------------------------
14:18:02.058 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.058 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.058 INFO  Funcotator - Inflater: IntelInflater
14:18:02.058 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.058 INFO  Funcotator - Requester pays: disabled
14:18:02.058 INFO  Funcotator - Initializing engine
14:18:02.059 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
14:18:02.082 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:18:02.083 INFO  Funcotator - Done initializing engine
14:18:02.083 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.083 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.083 INFO  Funcotator - Initializing data sources...
14:18:02.083 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/
14:18:02.083 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.083 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
14:18:02.083 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
14:18:02.083 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
14:18:02.083 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.083 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
14:18:02.083 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.084 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
14:18:02.084 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
14:18:02.084 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
14:18:02.085 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.085 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
14:18:02.092 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
14:18:02.101 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
14:18:02.108 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.112 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:02.112 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6565920524976874271.vcf
14:18:02.125 INFO  ProgressMeter - Starting traversal
14:18:02.125 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.138 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
14:18:02.138 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:18:02.138 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:02.143 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.211 INFO  Funcotator - ------------------------------------------------------------
14:18:02.211 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.211 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.211 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.211 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.211 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.211 INFO  Funcotator - ------------------------------------------------------------
14:18:02.211 INFO  Funcotator - ------------------------------------------------------------
14:18:02.211 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.211 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.211 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.211 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.211 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.211 INFO  Funcotator - Inflater: IntelInflater
14:18:02.211 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.211 INFO  Funcotator - Requester pays: disabled
14:18:02.211 INFO  Funcotator - Initializing engine
14:18:02.212 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
14:18:02.232 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:18:02.232 INFO  Funcotator - Done initializing engine
14:18:02.232 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.232 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.232 INFO  Funcotator - Initializing data sources...
14:18:02.232 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/
14:18:02.232 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.232 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
14:18:02.232 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
14:18:02.232 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
14:18:02.232 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.232 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
14:18:02.232 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.233 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
14:18:02.233 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
14:18:02.234 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
14:18:02.234 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.234 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
14:18:02.242 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/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:18:02.250 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
14:18:02.304 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.310 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:02.310 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7444155758737782632.vcf
14:18:02.322 INFO  ProgressMeter - Starting traversal
14:18:02.322 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.338 INFO  ProgressMeter -             unmapped              0.0                    32         120000.0
14:18:02.338 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:18:02.338 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:02.347 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.348 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6565920524976874271.vcf
14:18:02.360 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7444155758737782632.vcf
14:18:02.443 INFO  Funcotator - ------------------------------------------------------------
14:18:02.443 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.443 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.443 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.443 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.443 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.443 INFO  Funcotator - ------------------------------------------------------------
14:18:02.443 INFO  Funcotator - ------------------------------------------------------------
14:18:02.443 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.443 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.443 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.443 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.443 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.443 INFO  Funcotator - Inflater: IntelInflater
14:18:02.443 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.443 INFO  Funcotator - Requester pays: disabled
14:18:02.443 INFO  Funcotator - Initializing engine
14:18:02.444 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
14:18:02.445 INFO  Funcotator - Done initializing engine
14:18:02.445 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.445 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.445 INFO  Funcotator - Initializing data sources...
14:18:02.445 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.445 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.445 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
14:18:02.445 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
14:18:02.445 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
14:18:02.445 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.445 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
14:18:02.445 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.446 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
14:18:02.446 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
14:18:02.446 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
14:18:02.446 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.447 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
14:18:02.448 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
14:18:02.449 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
14:18:02.449 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.450 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.450 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.
14:18:02.450 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15754089897516139440.maf
14:18:02.450 INFO  ProgressMeter - Starting traversal
14:18:02.450 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.452 WARN  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
14:18:02.452 WARN  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
14:18:02.453 WARN  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
14:18:02.454 WARN  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=
14:18:02.454 WARN  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=
14:18:02.456 WARN  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=
14:18:02.456 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
14:18:02.456 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:18:02.456 WARN  Funcotator - ================================================================================
14:18:02.456 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:02.456 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:02.456 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:02.456 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:02.456 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:02.456 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:02.456 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:02.456 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:02.456 WARN  Funcotator -  run was misconfigured.     
14:18:02.456 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:02.456 WARN  Funcotator - ================================================================================
14:18:02.456 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:02.456 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.529 INFO  Funcotator - ------------------------------------------------------------
14:18:02.529 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.529 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.529 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.529 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.529 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.529 INFO  Funcotator - ------------------------------------------------------------
14:18:02.529 INFO  Funcotator - ------------------------------------------------------------
14:18:02.529 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.529 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.529 INFO  Funcotator - Inflater: IntelInflater
14:18:02.529 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.529 INFO  Funcotator - Requester pays: disabled
14:18:02.529 INFO  Funcotator - Initializing engine
14:18:02.530 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
14:18:02.531 INFO  Funcotator - Done initializing engine
14:18:02.531 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.531 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.531 INFO  Funcotator - Initializing data sources...
14:18:02.531 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.531 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.532 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
14:18:02.532 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
14:18:02.532 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
14:18:02.532 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.532 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
14:18:02.532 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.533 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
14:18:02.533 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
14:18:02.533 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
14:18:02.533 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.534 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
14:18:02.534 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
14:18:02.535 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
14:18:02.536 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.536 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.536 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.
14:18:02.536 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4292849918016278635.maf
14:18:02.537 INFO  ProgressMeter - Starting traversal
14:18:02.537 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.538 WARN  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
14:18:02.539 WARN  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
14:18:02.539 WARN  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
14:18:02.540 WARN  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=
14:18:02.540 WARN  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=
14:18:02.542 WARN  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=
14:18:02.542 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:18:02.542 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:18:02.542 WARN  Funcotator - ================================================================================
14:18:02.542 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:02.542 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:02.542 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:02.542 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:02.542 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:02.542 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:02.542 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:02.542 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:02.542 WARN  Funcotator -  run was misconfigured.     
14:18:02.542 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:02.542 WARN  Funcotator - ================================================================================
14:18:02.542 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:02.542 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.614 INFO  Funcotator - ------------------------------------------------------------
14:18:02.614 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.614 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.614 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.614 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.614 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.614 INFO  Funcotator - ------------------------------------------------------------
14:18:02.614 INFO  Funcotator - ------------------------------------------------------------
14:18:02.614 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.614 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.614 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.614 INFO  Funcotator - Inflater: IntelInflater
14:18:02.614 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.614 INFO  Funcotator - Requester pays: disabled
14:18:02.614 INFO  Funcotator - Initializing engine
14:18:02.615 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
14:18:02.616 INFO  Funcotator - Done initializing engine
14:18:02.616 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.616 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.616 INFO  Funcotator - Initializing data sources...
14:18:02.616 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.616 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.616 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
14:18:02.616 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
14:18:02.616 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
14:18:02.616 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.616 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
14:18:02.616 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.617 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
14:18:02.617 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
14:18:02.617 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
14:18:02.617 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.618 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
14:18:02.619 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
14:18:02.620 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
14:18:02.620 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.620 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.620 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.
14:18:02.620 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16451323237605489783.maf
14:18:02.621 INFO  ProgressMeter - Starting traversal
14:18:02.621 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.622 WARN  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
14:18:02.623 WARN  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
14:18:02.623 WARN  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
14:18:02.624 WARN  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=
14:18:02.624 WARN  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=
14:18:02.626 WARN  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=
14:18:02.626 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:18:02.626 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:18:02.626 WARN  Funcotator - ================================================================================
14:18:02.626 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:02.626 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:02.626 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:02.626 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:02.626 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:02.626 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:02.626 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:02.626 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:02.626 WARN  Funcotator -  run was misconfigured.     
14:18:02.626 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:02.626 WARN  Funcotator - ================================================================================
14:18:02.626 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:02.626 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.698 INFO  Funcotator - ------------------------------------------------------------
14:18:02.698 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.698 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.698 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.698 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.698 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.698 INFO  Funcotator - ------------------------------------------------------------
14:18:02.698 INFO  Funcotator - ------------------------------------------------------------
14:18:02.699 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.699 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.699 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.699 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.699 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.699 INFO  Funcotator - Inflater: IntelInflater
14:18:02.699 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.699 INFO  Funcotator - Requester pays: disabled
14:18:02.699 INFO  Funcotator - Initializing engine
14:18:02.700 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
14:18:02.701 INFO  Funcotator - Done initializing engine
14:18:02.701 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.701 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.701 INFO  Funcotator - Initializing data sources...
14:18:02.701 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.701 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.701 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_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:18:02.701 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_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:18:02.701 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
14:18:02.701 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.701 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_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:18:02.701 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.702 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
14:18:02.702 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_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:18:02.702 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
14:18:02.702 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.703 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
14:18:02.703 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
14:18:02.704 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
14:18:02.705 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.705 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.705 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.
14:18:02.705 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8877889573792415621.maf
14:18:02.706 INFO  ProgressMeter - Starting traversal
14:18:02.706 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.707 WARN  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
14:18:02.708 WARN  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
14:18:02.708 WARN  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
14:18:02.709 WARN  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=
14:18:02.709 WARN  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=
14:18:02.710 WARN  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=
14:18:02.711 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:18:02.711 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:18:02.711 WARN  Funcotator - ================================================================================
14:18:02.711 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:02.711 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:02.711 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:02.711 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:02.711 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:02.711 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:02.711 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:02.711 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:02.711 WARN  Funcotator -  run was misconfigured.     
14:18:02.711 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:02.711 WARN  Funcotator - ================================================================================
14:18:02.711 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:02.711 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.782 INFO  Funcotator - ------------------------------------------------------------
14:18:02.782 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.782 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.782 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.782 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.782 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.782 INFO  Funcotator - ------------------------------------------------------------
14:18:02.782 INFO  Funcotator - ------------------------------------------------------------
14:18:02.782 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.782 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.782 INFO  Funcotator - Inflater: IntelInflater
14:18:02.782 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.782 INFO  Funcotator - Requester pays: disabled
14:18:02.782 INFO  Funcotator - Initializing engine
14:18:02.783 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
14:18:02.784 INFO  Funcotator - Done initializing engine
14:18:02.784 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.784 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.784 INFO  Funcotator - Initializing data sources...
14:18:02.784 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.784 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.784 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
14:18:02.784 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
14:18:02.784 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
14:18:02.784 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.784 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
14:18:02.784 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.785 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
14:18:02.785 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
14:18:02.785 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
14:18:02.786 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.786 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
14:18:02.787 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
14:18:02.788 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
14:18:02.788 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.789 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.789 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.
14:18:02.789 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18294075901845524428.vcf
14:18:02.792 INFO  ProgressMeter - Starting traversal
14:18:02.792 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:02.802 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:18:02.802 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:18:02.802 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:18:02.804 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.805 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out18294075901845524428.vcf
14:18:02.877 INFO  Funcotator - ------------------------------------------------------------
14:18:02.877 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.877 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.877 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.877 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.877 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.877 INFO  Funcotator - ------------------------------------------------------------
14:18:02.877 INFO  Funcotator - ------------------------------------------------------------
14:18:02.877 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.877 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.877 INFO  Funcotator - Inflater: IntelInflater
14:18:02.877 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.877 INFO  Funcotator - Requester pays: disabled
14:18:02.877 INFO  Funcotator - Initializing engine
14:18:02.878 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
14:18:02.879 INFO  Funcotator - Done initializing engine
14:18:02.879 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.879 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.879 INFO  Funcotator - Initializing data sources...
14:18:02.879 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.879 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.879 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
14:18:02.879 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
14:18:02.879 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
14:18:02.879 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.879 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
14:18:02.879 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.880 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
14:18:02.880 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
14:18:02.881 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
14:18:02.881 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.881 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
14:18:02.882 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
14:18:02.883 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
14:18:02.883 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.884 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:02.884 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.
14:18:02.884 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17148384306838964322.maf
14:18:02.884 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:02.884 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:02.954 INFO  Funcotator - ------------------------------------------------------------
14:18:02.954 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:02.954 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:02.954 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:02.954 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:02.954 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:02 PM UTC
14:18:02.954 INFO  Funcotator - ------------------------------------------------------------
14:18:02.954 INFO  Funcotator - ------------------------------------------------------------
14:18:02.954 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:02.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:02.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:02.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:02.954 INFO  Funcotator - Deflater: IntelDeflater
14:18:02.954 INFO  Funcotator - Inflater: IntelInflater
14:18:02.954 INFO  Funcotator - GCS max retries/reopens: 20
14:18:02.954 INFO  Funcotator - Requester pays: disabled
14:18:02.954 INFO  Funcotator - Initializing engine
14:18:02.955 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
14:18:02.967 INFO  Funcotator - Done initializing engine
14:18:02.967 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:02.967 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:02.967 INFO  Funcotator - Initializing data sources...
14:18:02.967 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:02.967 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:02.967 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
14:18:02.967 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
14:18:02.967 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
14:18:02.967 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:02.968 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
14:18:02.968 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:02.968 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
14:18:02.968 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
14:18:02.969 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
14:18:02.969 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:02.969 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
14:18:02.977 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
14:18:02.986 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
14:18:02.994 INFO  Funcotator - Initializing Funcotator Engine...
14:18:02.998 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:02.998 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1795819895173880076.maf
14:18:02.999 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
14:18:02.999 INFO  ProgressMeter - Starting traversal
14:18:02.999 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:03.003 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)
14:18:03.003 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)
14:18:03.003 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.003 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:18:03.004 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:18:03.004 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:18:03.005 WARN  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+
14:18:03.009 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.009 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:18:03.009 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:18:03.009 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:18:03.009 WARN  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+
14:18:03.009 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)
14:18:03.010 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)
14:18:03.010 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.010 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:18:03.010 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:18:03.010 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:18:03.010 WARN  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+
14:18:03.011 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)
14:18:03.011 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)
14:18:03.011 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:18:03.011 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:18:03.011 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:18:03.011 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:18:03.011 WARN  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+
14:18:03.012 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.012 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:18:03.012 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:18:03.012 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:18:03.012 WARN  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+
14:18:03.013 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.013 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:18:03.013 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:18:03.013 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:18:03.013 WARN  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=
14:18:03.014 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)
14:18:03.014 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)
14:18:03.014 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:18:03.014 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:18:03.014 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:18:03.014 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:18:03.015 WARN  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=
14:18:03.015 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)
14:18:03.015 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)
14:18:03.015 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.015 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:18:03.015 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:18:03.016 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:18:03.016 WARN  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+
14:18:03.016 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:18:03.016 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:18:03.016 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:18:03.017 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:18:03.017 WARN  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+
14:18:03.017 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)
14:18:03.017 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)
14:18:03.017 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:18:03.017 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:18:03.018 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:18:03.018 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:18:03.018 WARN  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=
14:18:03.018 INFO  ProgressMeter -             unmapped              0.0                    10          31578.9
14:18:03.018 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:18:03.018 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:18:03.018 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
[June 2, 2025 at 2:18:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:03.168 INFO  Funcotator - ------------------------------------------------------------
14:18:03.168 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:03.168 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:03.168 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:03.168 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:03.168 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:03 PM UTC
14:18:03.168 INFO  Funcotator - ------------------------------------------------------------
14:18:03.168 INFO  Funcotator - ------------------------------------------------------------
14:18:03.168 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:03.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:03.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:03.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:03.168 INFO  Funcotator - Deflater: IntelDeflater
14:18:03.168 INFO  Funcotator - Inflater: IntelInflater
14:18:03.168 INFO  Funcotator - GCS max retries/reopens: 20
14:18:03.168 INFO  Funcotator - Requester pays: disabled
14:18:03.168 INFO  Funcotator - Initializing engine
14:18:03.169 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
14:18:03.171 INFO  Funcotator - Done initializing engine
14:18:03.171 INFO  Funcotator - Validating sequence dictionaries...
14:18:03.171 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3447717888
14:18:03.242 INFO  Funcotator - ------------------------------------------------------------
14:18:03.242 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:03.242 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:03.242 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:03.242 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:03.242 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:03 PM UTC
14:18:03.242 INFO  Funcotator - ------------------------------------------------------------
14:18:03.242 INFO  Funcotator - ------------------------------------------------------------
14:18:03.242 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:03.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:03.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:03.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:03.242 INFO  Funcotator - Deflater: IntelDeflater
14:18:03.242 INFO  Funcotator - Inflater: IntelInflater
14:18:03.242 INFO  Funcotator - GCS max retries/reopens: 20
14:18:03.242 INFO  Funcotator - Requester pays: disabled
14:18:03.242 INFO  Funcotator - Initializing engine
14:18:03.244 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
14:18:03.245 INFO  Funcotator - Done initializing engine
14:18:03.245 INFO  Funcotator - Validating sequence dictionaries...
14:18:03.245 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:03.245 INFO  Funcotator - Initializing data sources...
14:18:03.245 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:03.245 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:03.245 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
14:18:03.246 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
14:18:03.246 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
14:18:03.246 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
14:18:03.246 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
14:18:03.246 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
14:18:03.246 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
14:18:03.247 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
14:18:03.247 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
14:18:03.247 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
14:18:03.247 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
14:18:03.247 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
14:18:03.247 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
14:18:03.247 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
14:18:03.248 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
14:18:03.248 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:03.248 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
14:18:03.248 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
14:18:03.290 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
14:18:03.308 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
14:18:03.315 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
14:18:03.315 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
14:18:03.315 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
14:18:03.316 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
14:18:03.967 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
14:18:04.024 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
14:18:04.024 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:04.025 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
14:18:04.025 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
14:18:04.109 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:04.109 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
14:18:04.110 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
14:18:04.137 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
14:18:04.137 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	2025-06-02 14:18:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:04.138 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
14:18:04.138 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
14:18:04.139 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
14:18:04.139 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:04.139 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
14:18:04.142 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
14:18:04.144 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
14:18:04.146 INFO  Funcotator - Initializing Funcotator Engine...
14:18:04.147 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:18:04.147 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.
14:18:04.147 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator7535596855562933090.vcf
14:18:04.148 INFO  ProgressMeter - Starting traversal
14:18:04.148 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:06.371 INFO  ProgressMeter -             unmapped              0.0                   198           5344.1
14:18:06.371 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:18:06.371 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:18:06.380 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:06 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3462397952
14:18:06.449 INFO  Funcotator - ------------------------------------------------------------
14:18:06.449 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:06.449 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:06.449 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:06.449 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:06.449 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:06 PM UTC
14:18:06.449 INFO  Funcotator - ------------------------------------------------------------
14:18:06.449 INFO  Funcotator - ------------------------------------------------------------
14:18:06.449 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:06.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:06.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:06.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:06.449 INFO  Funcotator - Deflater: IntelDeflater
14:18:06.449 INFO  Funcotator - Inflater: IntelInflater
14:18:06.449 INFO  Funcotator - GCS max retries/reopens: 20
14:18:06.449 INFO  Funcotator - Requester pays: disabled
14:18:06.449 INFO  Funcotator - Initializing engine
14:18:06.451 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
14:18:06.452 INFO  Funcotator - Done initializing engine
14:18:06.452 INFO  Funcotator - Validating sequence dictionaries...
14:18:06.452 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:06.452 INFO  Funcotator - Initializing data sources...
14:18:06.452 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:06.452 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:06.452 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
14:18:06.452 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
14:18:06.453 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
14:18:06.453 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
14:18:06.453 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
14:18:06.453 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
14:18:06.453 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
14:18:06.453 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
14:18:06.453 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
14:18:06.454 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
14:18:06.454 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
14:18:06.454 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
14:18:06.454 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
14:18:06.454 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
14:18:06.454 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
14:18:06.454 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:06.454 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
14:18:06.455 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
14:18:06.496 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
14:18:06.514 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
14:18:06.520 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
14:18:06.520 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
14:18:06.521 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
14:18:06.521 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
14:18:07.076 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
14:18:07.116 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
14:18:07.116 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:07.116 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
14:18:07.117 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
14:18:07.199 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:07.199 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
14:18:07.200 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
14:18:07.227 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:18:07.227 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:18:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:07.227 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
14:18:07.228 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
14:18:07.228 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
14:18:07.228 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:07.229 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
14:18:07.231 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
14:18:07.233 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
14:18:07.235 INFO  Funcotator - Initializing Funcotator Engine...
14:18:07.235 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:18:07.235 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.
14:18:07.235 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator447146320777565559.maf
14:18:07.236 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
14:18:07.236 INFO  ProgressMeter - Starting traversal
14:18:07.236 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:09.452 INFO  ProgressMeter -             unmapped              0.0                   198           5361.0
14:18:09.452 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:18:09.453 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:18:09.453 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3462397952
14:18:09.523 INFO  Funcotator - ------------------------------------------------------------
14:18:09.523 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:09.523 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:09.523 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:09.523 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:09.523 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:09 PM UTC
14:18:09.523 INFO  Funcotator - ------------------------------------------------------------
14:18:09.523 INFO  Funcotator - ------------------------------------------------------------
14:18:09.523 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:09.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:09.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:09.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:09.523 INFO  Funcotator - Deflater: IntelDeflater
14:18:09.523 INFO  Funcotator - Inflater: IntelInflater
14:18:09.523 INFO  Funcotator - GCS max retries/reopens: 20
14:18:09.523 INFO  Funcotator - Requester pays: disabled
14:18:09.523 INFO  Funcotator - Initializing engine
14:18:09.551 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
14:18:09.571 INFO  Funcotator - Done initializing engine
14:18:09.571 INFO  Funcotator - Validating sequence dictionaries...
14:18:09.578 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:09.578 INFO  Funcotator - Initializing data sources...
14:18:09.578 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:09.578 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:09.578 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
14:18:09.578 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
14:18:09.578 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
14:18:09.578 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.579 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
14:18:09.580 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
14:18:09.580 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:09.580 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
14:18:09.649 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
14:18:09.667 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
14:18:09.674 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
14:18:09.674 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
14:18:09.674 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
14:18:09.674 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
14:18:10.216 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
14:18:10.282 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
14:18:10.282 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.282 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
14:18:10.283 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
14:18:10.284 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
14:18:10.284 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
14:18:10.284 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
14:18:10.284 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:10.285 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
14:18:10.286 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
14:18:10.288 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
14:18:10.289 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.292 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:10.293 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator17647933546465682062.vcf
14:18:10.293 INFO  ProgressMeter - Starting traversal
14:18:10.293 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.298 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:18:10.301 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3462397952
14:18:10.369 INFO  Funcotator - ------------------------------------------------------------
14:18:10.369 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.369 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.369 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.369 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.369 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.369 INFO  Funcotator - ------------------------------------------------------------
14:18:10.369 INFO  Funcotator - ------------------------------------------------------------
14:18:10.370 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.370 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.370 INFO  Funcotator - Inflater: IntelInflater
14:18:10.370 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.370 INFO  Funcotator - Requester pays: disabled
14:18:10.370 INFO  Funcotator - Initializing engine
14:18:10.372 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
14:18:10.372 INFO  Funcotator - Done initializing engine
14:18:10.372 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.372 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.372 INFO  Funcotator - Initializing data sources...
14:18:10.372 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
14:18:10.372 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.373 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
14:18:10.373 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
14:18:10.373 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
14:18:10.373 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.373 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
14:18:10.373 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.373 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
14:18:10.374 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
14:18:10.374 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
14:18:10.374 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:18:10.374 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
14:18:10.375 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
14:18:10.375 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
14:18:10.375 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.375 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.375 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.
14:18:10.375 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:10.376 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing13440093185952125009.vcf
14:18:10.376 INFO  ProgressMeter - Starting traversal
14:18:10.376 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.380 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
14:18:10.381 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:18:10.381 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
14:18:10.383 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.383 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing13440093185952125009.vcf
14:18:10.452 INFO  Funcotator - ------------------------------------------------------------
14:18:10.452 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.452 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.452 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.452 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.452 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.452 INFO  Funcotator - ------------------------------------------------------------
14:18:10.452 INFO  Funcotator - ------------------------------------------------------------
14:18:10.452 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.452 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.452 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.452 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.452 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.452 INFO  Funcotator - Inflater: IntelInflater
14:18:10.452 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.452 INFO  Funcotator - Requester pays: disabled
14:18:10.452 INFO  Funcotator - Initializing engine
14:18:10.453 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
14:18:10.454 INFO  Funcotator - Done initializing engine
14:18:10.454 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.454 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.454 INFO  Funcotator - Initializing data sources...
14:18:10.454 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.454 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.455 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
14:18:10.455 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
14:18:10.455 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
14:18:10.455 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.455 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
14:18:10.455 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.455 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
14:18:10.455 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
14:18:10.456 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
14:18:10.456 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.456 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
14:18:10.457 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
14:18:10.458 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
14:18:10.459 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.459 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.459 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.
14:18:10.459 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5011216668358914610.maf
14:18:10.459 INFO  ProgressMeter - Starting traversal
14:18:10.459 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.462 WARN  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=
14:18:10.462 WARN  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=
14:18:10.463 WARN  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=
14:18:10.463 WARN  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=
14:18:10.464 WARN  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=
14:18:10.464 WARN  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=
14:18:10.464 WARN  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=
14:18:10.465 WARN  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=
14:18:10.465 WARN  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=
14:18:10.466 WARN  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=
14:18:10.466 WARN  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=
14:18:10.466 WARN  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=
14:18:10.467 WARN  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=
14:18:10.467 WARN  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=
14:18:10.467 WARN  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=
14:18:10.467 WARN  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=
14:18:10.468 WARN  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=
14:18:10.468 WARN  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=
14:18:10.468 WARN  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=
14:18:10.469 WARN  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=
14:18:10.469 WARN  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=
14:18:10.469 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:18:10.469 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:18:10.469 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:18:10.469 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.472 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
14:18:10.473 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
14:18:10.550 INFO  Funcotator - ------------------------------------------------------------
14:18:10.550 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.550 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.550 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.550 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.550 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.550 INFO  Funcotator - ------------------------------------------------------------
14:18:10.550 INFO  Funcotator - ------------------------------------------------------------
14:18:10.550 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.550 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.550 INFO  Funcotator - Inflater: IntelInflater
14:18:10.550 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.550 INFO  Funcotator - Requester pays: disabled
14:18:10.550 INFO  Funcotator - Initializing engine
14:18:10.551 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
14:18:10.552 INFO  Funcotator - Done initializing engine
14:18:10.552 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.552 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.552 INFO  Funcotator - Initializing data sources...
14:18:10.552 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.552 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.552 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
14:18:10.553 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
14:18:10.553 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
14:18:10.553 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.553 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
14:18:10.553 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.553 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
14:18:10.553 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
14:18:10.554 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
14:18:10.554 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.554 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
14:18:10.555 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
14:18:10.556 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
14:18:10.557 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.557 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.557 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.
14:18:10.557 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1839020516091705893.vcf
14:18:10.560 INFO  ProgressMeter - Starting traversal
14:18:10.560 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.569 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
14:18:10.569 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:18:10.569 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:18:10.571 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.572 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1839020516091705893.vcf
14:18:10.643 INFO  Funcotator - ------------------------------------------------------------
14:18:10.643 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.643 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.643 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.643 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.643 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.643 INFO  Funcotator - ------------------------------------------------------------
14:18:10.643 INFO  Funcotator - ------------------------------------------------------------
14:18:10.643 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.643 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.643 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.643 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.643 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.643 INFO  Funcotator - Inflater: IntelInflater
14:18:10.643 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.643 INFO  Funcotator - Requester pays: disabled
14:18:10.643 INFO  Funcotator - Initializing engine
14:18:10.644 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
14:18:10.645 INFO  Funcotator - Done initializing engine
14:18:10.645 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.645 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.645 INFO  Funcotator - Initializing data sources...
14:18:10.645 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.645 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.645 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
14:18:10.645 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
14:18:10.645 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
14:18:10.645 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.645 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
14:18:10.645 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.646 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
14:18:10.646 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
14:18:10.647 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
14:18:10.647 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.647 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
14:18:10.649 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
14:18:10.650 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
14:18:10.650 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.650 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.650 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.
14:18:10.650 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:10.651 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9481162141790876824.vcf
14:18:10.651 INFO  ProgressMeter - Starting traversal
14:18:10.651 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.656 INFO  ProgressMeter -             unmapped              0.0                     5          60000.0
14:18:10.656 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:18:10.656 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:18:10.658 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.659 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9481162141790876824.vcf
14:18:10.729 INFO  Funcotator - ------------------------------------------------------------
14:18:10.729 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.729 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.729 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.729 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.729 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.729 INFO  Funcotator - ------------------------------------------------------------
14:18:10.729 INFO  Funcotator - ------------------------------------------------------------
14:18:10.729 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.729 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.729 INFO  Funcotator - Inflater: IntelInflater
14:18:10.729 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.729 INFO  Funcotator - Requester pays: disabled
14:18:10.729 INFO  Funcotator - Initializing engine
14:18:10.730 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
14:18:10.730 INFO  Funcotator - Done initializing engine
14:18:10.730 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.730 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.730 INFO  Funcotator - Initializing data sources...
14:18:10.731 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.731 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.731 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
14:18:10.731 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
14:18:10.731 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
14:18:10.731 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.731 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
14:18:10.731 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.732 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
14:18:10.732 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
14:18:10.732 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
14:18:10.732 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.732 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
14:18:10.733 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
14:18:10.734 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
14:18:10.735 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.735 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.735 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.
14:18:10.735 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:10.735 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7071155760579565685.vcf
14:18:10.736 INFO  ProgressMeter - Starting traversal
14:18:10.736 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.743 INFO  ProgressMeter -             unmapped              0.0                    15         128571.4
14:18:10.743 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:18:10.743 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:18:10.746 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.814 INFO  Funcotator - ------------------------------------------------------------
14:18:10.814 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.814 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.814 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.814 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.814 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.814 INFO  Funcotator - ------------------------------------------------------------
14:18:10.814 INFO  Funcotator - ------------------------------------------------------------
14:18:10.814 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.814 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.814 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.814 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.814 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.814 INFO  Funcotator - Inflater: IntelInflater
14:18:10.814 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.814 INFO  Funcotator - Requester pays: disabled
14:18:10.814 INFO  Funcotator - Initializing engine
14:18:10.815 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
14:18:10.815 INFO  Funcotator - Done initializing engine
14:18:10.815 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.815 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.815 INFO  Funcotator - Initializing data sources...
14:18:10.815 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.815 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.816 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
14:18:10.816 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
14:18:10.816 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
14:18:10.816 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.816 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
14:18:10.816 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.817 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
14:18:10.817 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
14:18:10.817 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
14:18:10.817 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.818 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
14:18:10.818 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
14:18:10.819 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
14:18:10.820 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.820 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.820 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.
14:18:10.820 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:10.820 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13207926399298710392.maf
14:18:10.820 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
14:18:10.820 INFO  ProgressMeter - Starting traversal
14:18:10.820 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.823 WARN  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=
14:18:10.823 WARN  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=
14:18:10.825 WARN  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=
14:18:10.825 WARN  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=
14:18:10.825 WARN  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=
14:18:10.826 WARN  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=
14:18:10.826 WARN  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=
14:18:10.826 WARN  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=
14:18:10.827 WARN  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=
14:18:10.827 WARN  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=
14:18:10.827 WARN  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=
14:18:10.828 WARN  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=
14:18:10.828 WARN  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=
14:18:10.828 WARN  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=
14:18:10.828 WARN  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=
14:18:10.829 INFO  ProgressMeter -             unmapped              0.0                    15         100000.0
14:18:10.829 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:18:10.829 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:18:10.829 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:10.830 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7071155760579565685.vcf
14:18:10.899 INFO  Funcotator - ------------------------------------------------------------
14:18:10.899 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:10.899 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:10.899 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:10.899 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:10.900 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:10 PM UTC
14:18:10.900 INFO  Funcotator - ------------------------------------------------------------
14:18:10.900 INFO  Funcotator - ------------------------------------------------------------
14:18:10.900 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:10.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:10.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:10.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:10.900 INFO  Funcotator - Deflater: IntelDeflater
14:18:10.900 INFO  Funcotator - Inflater: IntelInflater
14:18:10.900 INFO  Funcotator - GCS max retries/reopens: 20
14:18:10.900 INFO  Funcotator - Requester pays: disabled
14:18:10.900 INFO  Funcotator - Initializing engine
14:18:10.901 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
14:18:10.901 INFO  Funcotator - Done initializing engine
14:18:10.901 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:10.901 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:10.901 INFO  Funcotator - Initializing data sources...
14:18:10.901 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:10.901 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:10.901 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
14:18:10.902 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
14:18:10.902 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
14:18:10.902 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:10.902 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
14:18:10.902 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:10.902 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
14:18:10.903 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
14:18:10.903 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
14:18:10.903 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:10.903 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
14:18:10.904 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
14:18:10.905 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
14:18:10.906 INFO  Funcotator - Initializing Funcotator Engine...
14:18:10.906 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:10.906 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.
14:18:10.906 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:10.906 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4991054391911222145.vcf
14:18:10.906 INFO  ProgressMeter - Starting traversal
14:18:10.906 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:10.937 INFO  ProgressMeter -             unmapped              0.0                    57         110322.6
14:18:10.937 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:18:10.937 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:10.939 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:11.008 INFO  Funcotator - ------------------------------------------------------------
14:18:11.008 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:11.008 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:11.008 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:11.008 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:11.008 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:11 PM UTC
14:18:11.008 INFO  Funcotator - ------------------------------------------------------------
14:18:11.008 INFO  Funcotator - ------------------------------------------------------------
14:18:11.008 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:11.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:11.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:11.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:11.008 INFO  Funcotator - Deflater: IntelDeflater
14:18:11.008 INFO  Funcotator - Inflater: IntelInflater
14:18:11.008 INFO  Funcotator - GCS max retries/reopens: 20
14:18:11.008 INFO  Funcotator - Requester pays: disabled
14:18:11.008 INFO  Funcotator - Initializing engine
14:18:11.009 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
14:18:11.009 INFO  Funcotator - Done initializing engine
14:18:11.009 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:11.009 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:11.009 INFO  Funcotator - Initializing data sources...
14:18:11.009 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:11.009 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:11.009 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
14:18:11.009 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
14:18:11.010 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
14:18:11.010 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:11.010 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
14:18:11.010 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:11.010 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
14:18:11.010 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
14:18:11.011 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
14:18:11.011 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:11.011 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
14:18:11.012 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
14:18:11.013 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
14:18:11.014 INFO  Funcotator - Initializing Funcotator Engine...
14:18:11.014 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:11.014 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.
14:18:11.014 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:11.014 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13003287409384976888.maf
14:18:11.014 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
14:18:11.014 INFO  ProgressMeter - Starting traversal
14:18:11.014 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:11.016 WARN  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=
14:18:11.017 WARN  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=
14:18:11.017 WARN  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=
14:18:11.018 WARN  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=
14:18:11.019 WARN  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=
14:18:11.019 WARN  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=
14:18:11.020 WARN  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=
14:18:11.020 WARN  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=
14:18:11.021 WARN  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=
14:18:11.021 WARN  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=
14:18:11.022 WARN  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=
14:18:11.022 WARN  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=
14:18:11.022 WARN  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=
14:18:11.024 WARN  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=
14:18:11.024 WARN  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=
14:18:11.025 WARN  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=
14:18:11.025 WARN  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=
14:18:11.026 WARN  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=
14:18:11.026 WARN  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=
14:18:11.026 WARN  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=
14:18:11.028 WARN  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=
14:18:11.028 WARN  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=
14:18:11.029 WARN  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=
14:18:11.030 WARN  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=
14:18:11.030 WARN  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=
14:18:11.031 WARN  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=
14:18:11.032 WARN  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=
14:18:11.033 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
14:18:11.033 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:18:11.034 WARN  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=
14:18:11.034 WARN  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=
14:18:11.035 WARN  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=
14:18:11.035 WARN  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=
14:18:11.036 WARN  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=
14:18:11.036 WARN  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=
14:18:11.037 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
14:18:11.038 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:18:11.039 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 @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
14:18:11.040 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 @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
14:18:11.040 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 @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
14:18:11.040 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 @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
14:18:11.042 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 @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
14:18:11.042 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 @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
14:18:11.042 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 @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
14:18:11.043 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 @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
14:18:11.044 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 @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
14:18:11.045 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 @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
14:18:11.045 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 @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
14:18:11.046 WARN  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=
14:18:11.047 WARN  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=
14:18:11.048 WARN  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=
14:18:11.048 WARN  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=
14:18:11.048 WARN  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=
14:18:11.050 WARN  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=
14:18:11.050 WARN  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=
14:18:11.050 WARN  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=
14:18:11.051 WARN  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=
14:18:11.051 INFO  ProgressMeter -             unmapped              0.0                    57          92432.4
14:18:11.051 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:18:11.051 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:11.051 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:11 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:11.052 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4991054391911222145.vcf
14:18:11.126 INFO  Funcotator - ------------------------------------------------------------
14:18:11.126 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:11.126 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:11.126 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:11.126 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:11.126 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:11 PM UTC
14:18:11.126 INFO  Funcotator - ------------------------------------------------------------
14:18:11.126 INFO  Funcotator - ------------------------------------------------------------
14:18:11.126 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:11.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:11.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:11.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:11.126 INFO  Funcotator - Deflater: IntelDeflater
14:18:11.126 INFO  Funcotator - Inflater: IntelInflater
14:18:11.126 INFO  Funcotator - GCS max retries/reopens: 20
14:18:11.126 INFO  Funcotator - Requester pays: disabled
14:18:11.126 INFO  Funcotator - Initializing engine
14:18:11.127 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
14:18:11.128 INFO  Funcotator - Done initializing engine
14:18:11.128 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:11.128 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:11.128 INFO  Funcotator - Initializing data sources...
14:18:11.128 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:11.128 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:11.128 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
14:18:11.129 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
14:18:11.129 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
14:18:11.129 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
14:18:11.129 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
14:18:11.129 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
14:18:11.129 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
14:18:11.130 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
14:18:11.130 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
14:18:11.130 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
14:18:11.130 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
14:18:11.130 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
14:18:11.130 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
14:18:11.130 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
14:18:11.131 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
14:18:11.131 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:11.131 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
14:18:11.131 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
14:18:11.173 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
14:18:11.225 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
14:18:11.232 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
14:18:11.232 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
14:18:11.233 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
14:18:11.233 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
14:18:11.781 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
14:18:11.820 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
14:18:11.820 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:11.820 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
14:18:11.821 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
14:18:11.903 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:11.904 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
14:18:11.904 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
14:18:11.931 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
14:18:11.931 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	2025-06-02 14:18:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:11.932 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
14:18:11.932 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
14:18:11.933 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
14:18:11.933 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:11.933 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
14:18:11.935 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
14:18:11.938 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
14:18:11.940 INFO  Funcotator - Initializing Funcotator Engine...
14:18:11.940 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:11.940 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:11.940 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14212013330633253462.vcf
14:18:11.941 INFO  ProgressMeter - Starting traversal
14:18:11.941 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:22.050 INFO  ProgressMeter -        chr19:9077246              0.2                  1000           5935.3
14:18:29.903 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)
14:18:29.904 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)
14:18:30.764 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           6556.9
14:18:30.764 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:18:30.764 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:18:30.766 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:30 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.33 minutes.
Runtime.totalMemory()=3462397952
14:18:30.834 INFO  Funcotator - ------------------------------------------------------------
14:18:30.834 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:30.834 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:30.834 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:30.834 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:30.834 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:30 PM UTC
14:18:30.834 INFO  Funcotator - ------------------------------------------------------------
14:18:30.834 INFO  Funcotator - ------------------------------------------------------------
14:18:30.834 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:30.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:30.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:30.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:30.834 INFO  Funcotator - Deflater: IntelDeflater
14:18:30.834 INFO  Funcotator - Inflater: IntelInflater
14:18:30.835 INFO  Funcotator - GCS max retries/reopens: 20
14:18:30.835 INFO  Funcotator - Requester pays: disabled
14:18:30.835 INFO  Funcotator - Initializing engine
14:18:30.835 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
14:18:30.836 INFO  Funcotator - Done initializing engine
14:18:30.836 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:30.836 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:30.836 INFO  Funcotator - Initializing data sources...
14:18:30.836 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
14:18:30.836 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:30.836 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
14:18:30.836 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
14:18:30.836 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.837 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
14:18:30.838 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
14:18:30.838 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
14:18:30.838 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
14:18:30.838 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
14:18:30.838 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:30.838 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
14:18:30.839 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
14:18:30.881 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
14:18:30.900 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
14:18:30.907 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
14:18:30.908 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
14:18:30.908 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
14:18:30.908 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
14:18:31.501 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
14:18:31.540 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
14:18:31.540 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:31.541 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
14:18:31.541 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
14:18:31.624 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:31.624 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
14:18:31.624 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
14:18:31.652 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
14:18:31.652 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
WARNING	2025-06-02 14:18:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:31.652 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
14:18:31.653 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
14:18:31.653 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
14:18:31.653 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:18:31.654 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
14:18:31.656 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
14:18:31.658 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
14:18:31.660 INFO  Funcotator - Initializing Funcotator Engine...
14:18:31.660 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:31.660 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:31.660 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10942616795482710984.maf
14:18:31.660 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
14:18:31.661 INFO  ProgressMeter - Starting traversal
14:18:31.661 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:41.744 INFO  ProgressMeter -        chr19:9077246              0.2                  1000           5950.6
14:18:49.734 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)
14:18:49.736 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)
14:18:50.617 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           6510.9
14:18:50.617 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:18:50.617 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:18:50.617 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.33 minutes.
Runtime.totalMemory()=3462397952
14:18:50.618 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14212013330633253462.vcf
14:18:50.982 INFO  Funcotator - ------------------------------------------------------------
14:18:50.982 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:50.982 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:50.982 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:50.982 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:50.982 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:50 PM UTC
14:18:50.982 INFO  Funcotator - ------------------------------------------------------------
14:18:50.982 INFO  Funcotator - ------------------------------------------------------------
14:18:50.982 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:50.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:50.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:50.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:50.982 INFO  Funcotator - Deflater: IntelDeflater
14:18:50.982 INFO  Funcotator - Inflater: IntelInflater
14:18:50.982 INFO  Funcotator - GCS max retries/reopens: 20
14:18:50.982 INFO  Funcotator - Requester pays: disabled
14:18:50.982 INFO  Funcotator - Initializing engine
14:18:50.983 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
14:18:50.999 INFO  Funcotator - Done initializing engine
14:18:50.999 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:50.999 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:50.999 INFO  Funcotator - Initializing data sources...
14:18:50.999 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:50.999 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:50.999 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
14:18:50.999 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
14:18:50.999 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
14:18:50.999 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:50.999 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
14:18:50.999 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.000 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
14:18:51.000 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
14:18:51.001 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
14:18:51.001 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:51.001 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
14:18:51.008 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
14:18:51.016 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
14:18:51.024 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.030 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:51.030 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14850848104703089495.vcf
14:18:51.042 INFO  ProgressMeter - Starting traversal
14:18:51.042 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.069 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
14:18:51.069 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:18:51.069 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:51.074 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.142 INFO  Funcotator - ------------------------------------------------------------
14:18:51.142 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.142 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.142 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.142 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.142 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.142 INFO  Funcotator - ------------------------------------------------------------
14:18:51.142 INFO  Funcotator - ------------------------------------------------------------
14:18:51.142 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.142 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.142 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.142 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.142 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.142 INFO  Funcotator - Inflater: IntelInflater
14:18:51.142 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.142 INFO  Funcotator - Requester pays: disabled
14:18:51.142 INFO  Funcotator - Initializing engine
14:18:51.143 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
14:18:51.158 INFO  Funcotator - Done initializing engine
14:18:51.158 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.158 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.158 INFO  Funcotator - Initializing data sources...
14:18:51.158 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:51.158 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.158 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
14:18:51.158 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
14:18:51.159 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
14:18:51.159 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.159 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
14:18:51.159 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.159 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
14:18:51.159 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
14:18:51.160 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
14:18:51.160 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:51.160 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
14:18:51.168 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
14:18:51.176 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
14:18:51.183 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.188 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:18:51.188 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14521085582530433051.maf
14:18:51.188 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
14:18:51.188 INFO  ProgressMeter - Starting traversal
14:18:51.188 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.191 WARN  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=
14:18:51.196 WARN  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=
14:18:51.196 WARN  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+
14:18:51.196 WARN  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+
14:18:51.196 WARN  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+
14:18:51.197 WARN  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+
14:18:51.197 WARN  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=
14:18:51.197 WARN  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=
14:18:51.198 WARN  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=
14:18:51.198 WARN  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=
14:18:51.198 WARN  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=
14:18:51.198 WARN  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=
14:18:51.199 WARN  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=
14:18:51.199 WARN  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=
14:18:51.199 WARN  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=
14:18:51.199 WARN  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=
14:18:51.200 WARN  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=
14:18:51.200 WARN  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=
14:18:51.200 WARN  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=
14:18:51.201 WARN  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+
14:18:51.201 WARN  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
14:18:51.201 WARN  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=
14:18:51.202 WARN  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=
14:18:51.202 WARN  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=
14:18:51.202 WARN  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=
14:18:51.202 WARN  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=
14:18:51.203 WARN  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=
14:18:51.203 WARN  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=
14:18:51.203 WARN  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
14:18:51.203 WARN  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=
14:18:51.204 WARN  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=
14:18:51.204 WARN  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=
14:18:51.204 WARN  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=
14:18:51.204 WARN  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=
14:18:51.205 WARN  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=
14:18:51.205 WARN  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=
14:18:51.205 WARN  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=
14:18:51.205 WARN  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=
14:18:51.206 WARN  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=
14:18:51.206 WARN  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=
14:18:51.206 WARN  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=
14:18:51.207 WARN  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=
14:18:51.208 WARN  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=
14:18:51.208 WARN  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=
14:18:51.208 WARN  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=
14:18:51.208 WARN  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=
14:18:51.209 WARN  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+
14:18:51.209 WARN  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=
14:18:51.209 WARN  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=
14:18:51.209 WARN  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=
14:18:51.209 WARN  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=
14:18:51.210 WARN  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=
14:18:51.210 WARN  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=
14:18:51.210 WARN  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=
14:18:51.210 WARN  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=
14:18:51.211 WARN  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=
14:18:51.211 WARN  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=
14:18:51.211 WARN  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=
14:18:51.211 WARN  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=
14:18:51.211 WARN  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=
14:18:51.212 WARN  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=
14:18:51.212 WARN  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=
14:18:51.212 WARN  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=
14:18:51.212 WARN  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=
14:18:51.212 WARN  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=
14:18:51.213 WARN  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=
14:18:51.213 WARN  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=
14:18:51.213 WARN  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=
14:18:51.213 WARN  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=
14:18:51.213 WARN  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=
14:18:51.214 WARN  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=
14:18:51.214 WARN  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=
14:18:51.214 WARN  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=
14:18:51.214 WARN  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=
14:18:51.214 WARN  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=
14:18:51.215 WARN  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=
14:18:51.215 WARN  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=
14:18:51.215 WARN  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=
14:18:51.215 WARN  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=
14:18:51.215 WARN  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=
14:18:51.216 WARN  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=
14:18:51.216 WARN  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=
14:18:51.216 WARN  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=
14:18:51.216 WARN  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=
14:18:51.216 WARN  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=
14:18:51.217 WARN  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=
14:18:51.217 WARN  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=
14:18:51.217 WARN  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=
14:18:51.217 WARN  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=
14:18:51.218 WARN  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=
14:18:51.218 WARN  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=
14:18:51.218 WARN  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=
14:18:51.218 WARN  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=
14:18:51.218 WARN  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=
14:18:51.219 WARN  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=
14:18:51.219 WARN  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=
14:18:51.219 WARN  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=
14:18:51.219 WARN  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=
14:18:51.219 WARN  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=
14:18:51.220 WARN  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=
14:18:51.220 INFO  ProgressMeter -             unmapped              0.0                   100         187500.0
14:18:51.220 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:18:51.220 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:51.220 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.221 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14850848104703089495.vcf
14:18:51.352 INFO  Funcotator - ------------------------------------------------------------
14:18:51.352 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.352 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.352 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.352 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.352 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.352 INFO  Funcotator - ------------------------------------------------------------
14:18:51.352 INFO  Funcotator - ------------------------------------------------------------
14:18:51.352 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.352 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.352 INFO  Funcotator - Inflater: IntelInflater
14:18:51.352 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.352 INFO  Funcotator - Requester pays: disabled
14:18:51.352 INFO  Funcotator - Initializing engine
14:18:51.353 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
14:18:51.353 INFO  Funcotator - Done initializing engine
14:18:51.354 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.354 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.354 INFO  Funcotator - Initializing data sources...
14:18:51.354 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:51.354 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.354 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
14:18:51.354 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
14:18:51.354 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
14:18:51.354 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.354 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
14:18:51.354 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.355 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
14:18:51.355 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
14:18:51.355 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
14:18:51.355 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:51.356 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
14:18:51.356 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
14:18:51.357 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
14:18:51.358 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.358 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:51.358 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.
14:18:51.358 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:51.358 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7687405538839511624.vcf
14:18:51.359 INFO  ProgressMeter - Starting traversal
14:18:51.359 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.389 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
14:18:51.389 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:18:51.390 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:51.392 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.461 INFO  Funcotator - ------------------------------------------------------------
14:18:51.461 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.461 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.461 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.461 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.461 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.461 INFO  Funcotator - ------------------------------------------------------------
14:18:51.461 INFO  Funcotator - ------------------------------------------------------------
14:18:51.461 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.461 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.461 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.461 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.461 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.461 INFO  Funcotator - Inflater: IntelInflater
14:18:51.461 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.461 INFO  Funcotator - Requester pays: disabled
14:18:51.461 INFO  Funcotator - Initializing engine
14:18:51.462 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
14:18:51.462 INFO  Funcotator - Done initializing engine
14:18:51.462 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.462 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.462 INFO  Funcotator - Initializing data sources...
14:18:51.462 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:51.462 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.463 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
14:18:51.463 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
14:18:51.463 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
14:18:51.463 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.463 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
14:18:51.463 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.463 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
14:18:51.464 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
14:18:51.464 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
14:18:51.464 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:51.464 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
14:18:51.465 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
14:18:51.466 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
14:18:51.467 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.467 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:51.467 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.
14:18:51.467 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:18:51.467 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3326566290914867379.maf
14:18:51.467 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
14:18:51.467 INFO  ProgressMeter - Starting traversal
14:18:51.467 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.469 WARN  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=
14:18:51.470 WARN  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=
14:18:51.470 WARN  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=
14:18:51.470 WARN  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=
14:18:51.472 WARN  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=
14:18:51.472 WARN  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=
14:18:51.472 WARN  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=
14:18:51.473 WARN  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=
14:18:51.474 WARN  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=
14:18:51.474 WARN  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=
14:18:51.474 WARN  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=
14:18:51.475 WARN  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=
14:18:51.475 WARN  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=
14:18:51.476 WARN  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=
14:18:51.477 WARN  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=
14:18:51.477 WARN  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=
14:18:51.478 WARN  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=
14:18:51.478 WARN  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=
14:18:51.479 WARN  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=
14:18:51.479 WARN  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=
14:18:51.480 WARN  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=
14:18:51.480 WARN  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=
14:18:51.482 WARN  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=
14:18:51.482 WARN  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=
14:18:51.482 WARN  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=
14:18:51.484 WARN  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=
14:18:51.484 WARN  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=
14:18:51.485 WARN  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=
14:18:51.486 WARN  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=
14:18:51.486 WARN  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=
14:18:51.486 WARN  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=
14:18:51.488 WARN  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=
14:18:51.488 WARN  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=
14:18:51.488 WARN  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=
14:18:51.489 WARN  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=
14:18:51.490 WARN  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=
14:18:51.490 WARN  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=
14:18:51.491 WARN  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=
14:18:51.492 WARN  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=
14:18:51.492 WARN  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=
14:18:51.493 WARN  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=
14:18:51.494 WARN  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=
14:18:51.494 WARN  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=
14:18:51.495 WARN  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=
14:18:51.495 WARN  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=
14:18:51.496 WARN  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=
14:18:51.497 WARN  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=
14:18:51.497 WARN  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=
14:18:51.497 WARN  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=
14:18:51.498 WARN  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=
14:18:51.499 WARN  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=
14:18:51.499 WARN  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=
14:18:51.500 WARN  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=
14:18:51.501 WARN  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=
14:18:51.501 WARN  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=
14:18:51.502 WARN  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=
14:18:51.502 WARN  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=
14:18:51.502 INFO  ProgressMeter -             unmapped              0.0                    57          97714.3
14:18:51.502 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:18:51.502 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:18:51.503 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.503 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7687405538839511624.vcf
14:18:51.601 INFO  Funcotator - ------------------------------------------------------------
14:18:51.601 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.601 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.601 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.601 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.601 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.601 INFO  Funcotator - ------------------------------------------------------------
14:18:51.601 INFO  Funcotator - ------------------------------------------------------------
14:18:51.601 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.601 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.601 INFO  Funcotator - Inflater: IntelInflater
14:18:51.601 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.601 INFO  Funcotator - Requester pays: disabled
14:18:51.601 INFO  Funcotator - Initializing engine
14:18:51.602 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
14:18:51.603 INFO  Funcotator - Done initializing engine
14:18:51.603 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.603 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.603 INFO  Funcotator - Initializing data sources...
14:18:51.603 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
14:18:51.603 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.604 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
14:18:51.604 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
14:18:51.604 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
14:18:51.604 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.604 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
14:18:51.604 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.605 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
14:18:51.605 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
14:18:51.605 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
14:18:51.605 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:18:51.606 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
14:18:51.606 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
14:18:51.607 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
14:18:51.608 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.608 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:51.608 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.
14:18:51.608 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4390317169200814361.maf
14:18:51.609 INFO  ProgressMeter - Starting traversal
14:18:51.609 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.611 WARN  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=
14:18:51.612 WARN  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=
14:18:51.612 WARN  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=
14:18:51.613 WARN  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=
14:18:51.614 WARN  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=
14:18:51.614 WARN  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=
14:18:51.614 WARN  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=
14:18:51.615 WARN  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=
14:18:51.615 WARN  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=
14:18:51.616 WARN  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=
14:18:51.616 WARN  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=
14:18:51.616 WARN  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=
14:18:51.617 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 @ 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=
14:18:51.617 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 @ 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=
14:18:51.617 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 @ 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=
14:18:51.617 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 @ 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=
14:18:51.618 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 @ 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=
14:18:51.618 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 @ 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=
14:18:51.618 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 @ 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=
14:18:51.619 WARN  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=
14:18:51.619 WARN  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=
14:18:51.619 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:18:51.619 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:18:51.619 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:18:51.619 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.693 INFO  Funcotator - ------------------------------------------------------------
14:18:51.693 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.693 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.693 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.693 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.693 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.693 INFO  Funcotator - ------------------------------------------------------------
14:18:51.693 INFO  Funcotator - ------------------------------------------------------------
14:18:51.693 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.693 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.693 INFO  Funcotator - Inflater: IntelInflater
14:18:51.693 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.693 INFO  Funcotator - Requester pays: disabled
14:18:51.693 INFO  Funcotator - Initializing engine
14:18:51.694 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
14:18:51.695 INFO  Funcotator - Done initializing engine
14:18:51.695 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.695 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.695 INFO  Funcotator - Initializing data sources...
14:18:51.695 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:18:51.695 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.695 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
14:18:51.695 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
14:18:51.696 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
14:18:51.696 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.696 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:51.696 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
14:18:51.696 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
14:18:51.724 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
14:18:51.724 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	2025-06-02 14:18:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:51.724 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
14:18:51.724 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.725 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
14:18:51.725 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
14:18:51.726 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.726 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:51.726 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.
14:18:51.726 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3079221856306933590.vcf
14:18:51.729 INFO  ProgressMeter - Starting traversal
14:18:51.729 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.733 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
14:18:51.733 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:18:51.733 WARN  Funcotator - ================================================================================
14:18:51.733 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:51.733 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:51.733 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:51.733 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:51.733 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:51.733 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:51.733 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:51.733 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:51.733 WARN  Funcotator -  run was misconfigured.     
14:18:51.733 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:51.733 WARN  Funcotator - ================================================================================
14:18:51.734 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.734 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3079221856306933590.vcf
14:18:51.806 INFO  Funcotator - ------------------------------------------------------------
14:18:51.806 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
14:18:51.806 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:18:51.806 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:18:51.806 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:18:51.806 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:18:51 PM UTC
14:18:51.806 INFO  Funcotator - ------------------------------------------------------------
14:18:51.806 INFO  Funcotator - ------------------------------------------------------------
14:18:51.806 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:18:51.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:18:51.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:18:51.806 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:18:51.806 INFO  Funcotator - Deflater: IntelDeflater
14:18:51.806 INFO  Funcotator - Inflater: IntelInflater
14:18:51.806 INFO  Funcotator - GCS max retries/reopens: 20
14:18:51.806 INFO  Funcotator - Requester pays: disabled
14:18:51.806 INFO  Funcotator - Initializing engine
14:18:51.808 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
14:18:51.809 INFO  Funcotator - Done initializing engine
14:18:51.809 INFO  Funcotator - Skipping sequence dictionary validation.
14:18:51.809 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:18:51.809 INFO  Funcotator - Initializing data sources...
14:18:51.809 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:18:51.809 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:18:51.809 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
14:18:51.809 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
14:18:51.809 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
14:18:51.809 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:18:51.809 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:18:51.810 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
14:18:51.810 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
14:18:51.837 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
14:18:51.838 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	2025-06-02 14:18:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:18:51.838 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
14:18:51.838 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:18:51.839 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
14:18:51.839 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
14:18:51.839 INFO  Funcotator - Initializing Funcotator Engine...
14:18:51.839 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:18:51.839 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.
14:18:51.840 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3925922920669301924.vcf
14:18:51.843 INFO  ProgressMeter - Starting traversal
14:18:51.843 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:18:51.845 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
14:18:51.845 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:18:51.845 WARN  Funcotator - ================================================================================
14:18:51.845 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:18:51.845 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:18:51.845 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:18:51.845 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:18:51.845 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:18:51.845 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:18:51.845 WARN  Funcotator - --------------------------------------------------------------------------------
14:18:51.845 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:18:51.845 WARN  Funcotator -  run was misconfigured.     
14:18:51.845 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:18:51.845 WARN  Funcotator - ================================================================================
14:18:51.845 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:18:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3462397952
14:18:51.846 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3925922920669301924.vcf