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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
tests
failures
ignored
1m41.46s
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/funcotatorTmpFolder11807019712358758818/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)	1.123s	passed
exhaustiveArgumentTest[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.288s	passed
exhaustiveArgumentTest[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	1.023s	passed
exhaustiveArgumentTest[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.133s	passed
exhaustiveArgumentTest[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	1.047s	passed
exhaustiveArgumentTest[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.187s	passed
exhaustiveArgumentTest[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	1.013s	passed
exhaustiveArgumentTest[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.071s	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)	6.454s	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)	5.641s	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)	2.004s	passed
nonTrivialLargeDataValidationTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, hg38, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf, [], false)	2.024s	passed
nonTrivialLargeDataValidationTest[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf, [], true)	12.778s	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)	5.889s	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)	0.072s	passed
testCanAnnotateHg38ClinvarAndGencodeV28	0.173s	passed
testCanAnnotateMixedContigHg19Clinvar	0.098s	passed
testCanAnnotateSpanningDeletions	0.156s	passed
testCanCreateNonLocatableFuncotations	1.011s	passed
testCanHandleSymbollicAlleleFuncotations	1.057s	passed
testCustomVariantClassificationOrder	1.071s	passed
testEColiFuncotations	0.101s	passed
testEnsureDbSnpInMaf	0.079s	passed
testExclusionFromDatasourceVcfToVcf	0.253s	passed
testFilterParsing	0.112s	passed
testFuncotatorWithoutValidatingResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	0.918s	passed
testFuncotatorWithoutValidatingResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.062s	passed
testFuncotatorWithoutValidatingResults[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	0.953s	passed
testFuncotatorWithoutValidatingResults[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	0.984s	passed
testFuncotatorWithoutValidatingResults[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	0.935s	passed
testFuncotatorWithoutValidatingResults[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	0.991s	passed
testFuncotatorWithoutValidatingResults[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder11807019712358758818/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)	0.901s	passed
testFuncotatorWithoutValidatingResults[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder5238602792254396621/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)	1.033s	passed
testMANESelectAnnotationDifferencesAndGencodeV43	0.324s	passed
testMafCustomCountFieldsTumorOnly[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf)	0.082s	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)	0.086s	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	0.093s	passed
testMoreThanOneTNPair	0.075s	passed
testNoSpanningDeletionWriteWithMAF	0.131s	passed
testNoVariantsProduceMaf	0.076s	passed
testSequenceDictionaryCheck	0.068s	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)	5.926s	passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput	0.858s	passed
testVCFColumnsArentShuffled	0.083s	passed
testVCFToMAFPreservesFields	0.098s	passed
testVCFToVCFPreservesFields	0.099s	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/funcotatorTmpFolder14820340929907095222/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15)	0.181s	passed
testVcfMafConcordance[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder14820340929907095222/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.232s	passed
testVcfMafConcordance[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder5238602792254396621/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057)	36.241s	passed
testVcfMafConcordance[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder5143185011346524015/hg38.3.fasta, hg38, [Gencode_28_hugoSymbol, Gencode_28_ncbiBuild, Gencode_28_chromosome, Gencode_28_start, Gencode_28_end, Gencode_28_variantClassification, Gencode_28_variantType, Gencode_28_refAllele, Gencode_28_tumorSeqAllele1, Gencode_28_tumorSeqAllele2, Gencode_28_genomeChange, Gencode_28_annotationTranscript, Gencode_28_transcriptStrand, Gencode_28_transcriptExon, Gencode_28_transcriptPos, Gencode_28_cDnaChange, Gencode_28_codonChange, Gencode_28_proteinChange, Gencode_28_gcContent, Gencode_28_referenceContext, Gencode_28_otherTranscripts], [Hugo_Symbol, NCBI_Build, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Genome_Change, Annotation_Transcript, Transcript_Strand, Transcript_Exon, Transcript_Position, cDNA_Change, Codon_Change, Protein_Change, gc_content, ref_context, Other_Transcripts], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, false, 104)	0.364s	passed
testVcfMafConcordance[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder14820340929907095222/b37.3.fasta, hg19, [Gencode_19_hugoSymbol, Gencode_19_ncbiBuild, Gencode_19_chromosome, Gencode_19_start, Gencode_19_end, Gencode_19_variantClassification, Gencode_19_variantType, Gencode_19_refAllele, Gencode_19_tumorSeqAllele1, Gencode_19_tumorSeqAllele2, Gencode_19_genomeChange, Gencode_19_annotationTranscript, Gencode_19_transcriptStrand, Gencode_19_transcriptExon, Gencode_19_transcriptPos, Gencode_19_cDnaChange, Gencode_19_codonChange, Gencode_19_proteinChange, Gencode_19_gcContent, Gencode_19_referenceContext, Gencode_19_otherTranscripts], [Hugo_Symbol, NCBI_Build, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Genome_Change, Annotation_Transcript, Transcript_Strand, Transcript_Exon, Transcript_Position, cDNA_Change, Codon_Change, Protein_Change, gc_content, ref_context, Other_Transcripts], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.234s	passed
testVcfToMafHonorsExcludedFields	0.088s	passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified	0.114s	passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations	0.118s	passed
Standard error

15:40:56.881 INFO  Funcotator - ------------------------------------------------------------
15:40:56.881 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:40:56.881 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:40:56.881 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:40:56.881 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:40:56.881 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:40:56 PM UTC
15:40:56.881 INFO  Funcotator - ------------------------------------------------------------
15:40:56.881 INFO  Funcotator - ------------------------------------------------------------
15:40:56.881 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:40:56.881 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:40:56.881 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:40:56.881 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:40:56.881 INFO  Funcotator - Deflater: IntelDeflater
15:40:56.881 INFO  Funcotator - Inflater: IntelInflater
15:40:56.881 INFO  Funcotator - GCS max retries/reopens: 20
15:40:56.881 INFO  Funcotator - Requester pays: disabled
15:40:56.881 INFO  Funcotator - Initializing engine
15:40:56.882 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
15:40:56.883 INFO  Funcotator - Done initializing engine
15:40:56.883 INFO  Funcotator - Skipping sequence dictionary validation.
15:40:56.883 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:40:56.883 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4800656416481676518/TranscriptIdFile.txt
15:40:56.883 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:40:56.883 INFO  FuncotatorEngine - Transcript parsing complete.
15:40:56.883 INFO  Funcotator - Initializing data sources...
15:40:56.883 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:40:56.884 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:40:56.884 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
15:40:56.884 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
15:40:56.885 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
15:40:56.885 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
15:40:56.885 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
15:40:56.885 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
15:40:56.886 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
15:40:56.886 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
15:40:56.886 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
15:40:56.886 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
15:40:56.886 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
15:40:56.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:56.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:40:56.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:40:56.887 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
15:40:56.887 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:40:56.888 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
15:40:56.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:40:57.015 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:40:57.034 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
15:40:57.041 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
15:40:57.041 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
15:40:57.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:40:57.042 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
15:40:57.637 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
15:40:57.676 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
15:40:57.676 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:40:57.677 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
15:40:57.678 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
15:40:57.771 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:40:57.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:57.772 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
15:40:57.800 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:57.800 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:40:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:40:57.801 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
15:40:57.801 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
15:40:57.802 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
15:40:57.802 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:40:57.803 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
15:40:57.805 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
15:40:57.808 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
15:40:57.810 INFO  Funcotator - Initializing Funcotator Engine...
15:40:57.810 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
15:40:57.811 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:40:57.811 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:40:57.811 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:40:57.811 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:40:57.811 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:40:57.811 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:40:57.811 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:40:57.812 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:40:57.813 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:40:57.814 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:40:57.814 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:40:57.814 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.32075558108129267436.vcf
15:40:57.815 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
15:40:57.819 INFO  ProgressMeter - Starting traversal
15:40:57.819 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:40:57.928 INFO  ProgressMeter -             unmapped              0.0                     3           1651.4
15:40:57.928 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:40:57.928 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:40:57.932 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:40:57 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2290089984
15:40:58.011 INFO  Funcotator - ------------------------------------------------------------
15:40:58.012 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:40:58.012 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:40:58.012 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:40:58.012 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:40:58.012 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:40:58 PM UTC
15:40:58.012 INFO  Funcotator - ------------------------------------------------------------
15:40:58.012 INFO  Funcotator - ------------------------------------------------------------
15:40:58.012 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:40:58.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:40:58.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:40:58.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:40:58.012 INFO  Funcotator - Deflater: IntelDeflater
15:40:58.012 INFO  Funcotator - Inflater: IntelInflater
15:40:58.012 INFO  Funcotator - GCS max retries/reopens: 20
15:40:58.012 INFO  Funcotator - Requester pays: disabled
15:40:58.012 INFO  Funcotator - Initializing engine
15:40:58.014 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
15:40:58.015 INFO  Funcotator - Done initializing engine
15:40:58.015 INFO  Funcotator - Skipping sequence dictionary validation.
15:40:58.015 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:40:58.015 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6657943910740269125/TranscriptIdFile.txt
15:40:58.015 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:40:58.015 INFO  FuncotatorEngine - Transcript parsing complete.
15:40:58.015 INFO  Funcotator - Initializing data sources...
15:40:58.015 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:40:58.015 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:40:58.015 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
15:40:58.016 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
15:40:58.016 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:40:58.016 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
15:40:58.016 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
15:40:58.017 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
15:40:58.017 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
15:40:58.017 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
15:40:58.017 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
15:40:58.017 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
15:40:58.018 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
15:40:58.018 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:58.018 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
15:40:58.018 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:40:58.018 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:40:58.018 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:40:58.018 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
15:40:58.019 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
15:40:58.063 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
15:40:58.083 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
15:40:58.091 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
15:40:58.091 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
15:40:58.091 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
15:40:58.091 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
15:40:58.717 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
15:40:58.756 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
15:40:58.756 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:40:58.757 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
15:40:58.758 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:40:58.849 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:40:58.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:58.850 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
15:40:58.877 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:40:58.877 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:40:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:40:58.877 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
15:40:58.878 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
15:40:58.878 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
15:40:58.879 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:40:58.879 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
15:40:58.882 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
15:40:58.884 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
15:40:58.887 INFO  Funcotator - Initializing Funcotator Engine...
15:40:58.887 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:40:58.887 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:40:58.887 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.416977113135137034662.vcf
15:40:58.888 INFO  ProgressMeter - Starting traversal
15:40:58.888 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:40:59.219 INFO  ProgressMeter -             unmapped              0.0                     4            725.1
15:40:59.219 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:40:59.219 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:40:59.219 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:40:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2290089984
15:40:59.289 INFO  Funcotator - ------------------------------------------------------------
15:40:59.289 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:40:59.289 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:40:59.289 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:40:59.289 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:40:59.289 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:40:59 PM UTC
15:40:59.289 INFO  Funcotator - ------------------------------------------------------------
15:40:59.289 INFO  Funcotator - ------------------------------------------------------------
15:40:59.289 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:40:59.289 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:40:59.290 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:40:59.290 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:40:59.290 INFO  Funcotator - Deflater: IntelDeflater
15:40:59.290 INFO  Funcotator - Inflater: IntelInflater
15:40:59.290 INFO  Funcotator - GCS max retries/reopens: 20
15:40:59.290 INFO  Funcotator - Requester pays: disabled
15:40:59.290 INFO  Funcotator - Initializing engine
15:40:59.290 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
15:40:59.291 INFO  Funcotator - Done initializing engine
15:40:59.291 INFO  Funcotator - Skipping sequence dictionary validation.
15:40:59.291 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:40:59.291 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder3366330451745418747/TranscriptIdFile.txt
15:40:59.291 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:40:59.291 INFO  FuncotatorEngine - Transcript parsing complete.
15:40:59.291 INFO  Funcotator - Initializing data sources...
15:40:59.291 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:40:59.292 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:40:59.292 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
15:40:59.292 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
15:40:59.292 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
15:40:59.293 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
15:40:59.293 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
15:40:59.293 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
15:40:59.293 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
15:40:59.293 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
15:40:59.294 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
15:40:59.294 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
15:40:59.294 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
15:40:59.294 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
15:40:59.294 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
15:40:59.295 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
15:40:59.295 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
15:40:59.295 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:40:59.295 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:40:59.295 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
15:40:59.338 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:40:59.357 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
15:40:59.365 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
15:40:59.365 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
15:40:59.366 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
15:40:59.366 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
15:41:00.050 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
15:41:00.089 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
15:41:00.089 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:00.090 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
15:41:00.091 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
15:41:00.173 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:00.174 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:00.174 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
15:41:00.202 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:00.202 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:00.203 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
15:41:00.203 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
15:41:00.204 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
15:41:00.204 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:00.205 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
15:41:00.207 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
15:41:00.210 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
15:41:00.212 INFO  Funcotator - Initializing Funcotator Engine...
15:41:00.212 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
15:41:00.212 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:00.212 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:00.212 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:00.212 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:00.212 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:00.213 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:00.214 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:00.214 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:00.214 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.36949671744897930862.vcf
15:41:00.214 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
15:41:00.215 INFO  ProgressMeter - Starting traversal
15:41:00.215 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:00.240 INFO  ProgressMeter -             unmapped              0.0                     3           7200.0
15:41:00.240 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:00.240 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:00.243 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2290089984
15:41:00.315 INFO  Funcotator - ------------------------------------------------------------
15:41:00.315 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:00.315 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:00.315 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:00.315 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:00.315 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:00 PM UTC
15:41:00.315 INFO  Funcotator - ------------------------------------------------------------
15:41:00.315 INFO  Funcotator - ------------------------------------------------------------
15:41:00.315 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:00.315 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:00.315 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:00.315 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:00.315 INFO  Funcotator - Deflater: IntelDeflater
15:41:00.315 INFO  Funcotator - Inflater: IntelInflater
15:41:00.315 INFO  Funcotator - GCS max retries/reopens: 20
15:41:00.315 INFO  Funcotator - Requester pays: disabled
15:41:00.315 INFO  Funcotator - Initializing engine
15:41:00.316 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
15:41:00.317 INFO  Funcotator - Done initializing engine
15:41:00.317 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:00.317 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:00.317 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13316154351140467527/TranscriptIdFile.txt
15:41:00.317 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:41:00.317 INFO  FuncotatorEngine - Transcript parsing complete.
15:41:00.317 INFO  Funcotator - Initializing data sources...
15:41:00.317 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:00.317 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:00.318 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
15:41:00.318 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
15:41:00.318 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
15:41:00.318 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
15:41:00.318 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
15:41:00.319 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
15:41:00.319 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
15:41:00.319 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
15:41:00.319 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
15:41:00.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:41:00.320 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
15:41:00.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:00.320 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
15:41:00.320 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
15:41:00.321 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
15:41:00.321 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:00.321 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
15:41:00.321 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
15:41:00.367 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
15:41:00.386 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
15:41:00.394 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
15:41:00.394 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
15:41:00.394 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
15:41:00.395 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
15:41:01.047 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
15:41:01.086 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
15:41:01.086 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:01.087 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
15:41:01.088 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
15:41:01.170 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:01.171 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:01.171 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
15:41:01.199 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
15:41:01.199 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
WARNING	2025-05-27 15:41:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:01.199 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
15:41:01.200 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
15:41:01.200 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
15:41:01.200 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:01.201 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
15:41:01.203 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
15:41:01.206 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:01.208 INFO  Funcotator - Initializing Funcotator Engine...
15:41:01.208 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:01.208 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:01.208 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.411585062862280203471.vcf
15:41:01.209 INFO  ProgressMeter - Starting traversal
15:41:01.209 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:01.375 INFO  ProgressMeter -             unmapped              0.0                     4           1445.8
15:41:01.375 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:01.375 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:01.376 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2290089984
15:41:01.450 INFO  Funcotator - ------------------------------------------------------------
15:41:01.450 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:01.450 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:01.450 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:01.450 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:01.450 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:01 PM UTC
15:41:01.450 INFO  Funcotator - ------------------------------------------------------------
15:41:01.450 INFO  Funcotator - ------------------------------------------------------------
15:41:01.450 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:01.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:01.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:01.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:01.451 INFO  Funcotator - Deflater: IntelDeflater
15:41:01.451 INFO  Funcotator - Inflater: IntelInflater
15:41:01.451 INFO  Funcotator - GCS max retries/reopens: 20
15:41:01.451 INFO  Funcotator - Requester pays: disabled
15:41:01.451 INFO  Funcotator - Initializing engine
15:41:01.451 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
15:41:01.452 INFO  Funcotator - Done initializing engine
15:41:01.452 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:01.452 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:01.452 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder14132378736698213491/TranscriptIdFile.txt
15:41:01.452 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:41:01.452 INFO  FuncotatorEngine - Transcript parsing complete.
15:41:01.452 INFO  Funcotator - Initializing data sources...
15:41:01.452 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:01.452 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:01.453 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
15:41:01.453 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
15:41:01.453 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
15:41:01.453 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
15:41:01.453 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
15:41:01.454 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
15:41:01.454 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
15:41:01.454 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
15:41:01.454 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
15:41:01.454 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
15:41:01.454 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
15:41:01.455 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:01.455 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
15:41:01.455 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
15:41:01.455 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
15:41:01.455 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:01.455 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
15:41:01.456 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
15:41:01.498 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
15:41:01.517 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
15:41:01.525 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
15:41:01.525 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
15:41:01.526 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
15:41:01.526 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
15:41:02.230 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
15:41:02.269 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
15:41:02.269 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:02.269 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
15:41:02.270 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
15:41:02.353 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:02.353 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:02.354 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
15:41:02.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:02.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:02.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:41:02.382 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
15:41:02.382 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
15:41:02.382 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:02.383 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
15:41:02.386 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
15:41:02.389 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
15:41:02.391 INFO  Funcotator - Initializing Funcotator Engine...
15:41:02.391 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
15:41:02.392 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:02.392 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:02.392 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:02.392 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:02.393 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:02.393 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:02.393 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.37291100146729800890.maf
15:41:02.396 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
15:41:02.397 INFO  ProgressMeter - Starting traversal
15:41:02.397 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:02.423 INFO  ProgressMeter -             unmapped              0.0                     3           6923.1
15:41:02.423 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:02.423 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:02.423 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2462056448
15:41:02.491 INFO  Funcotator - ------------------------------------------------------------
15:41:02.491 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:02.491 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:02.492 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:02.492 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:02.492 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:02 PM UTC
15:41:02.492 INFO  Funcotator - ------------------------------------------------------------
15:41:02.492 INFO  Funcotator - ------------------------------------------------------------
15:41:02.492 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:02.492 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:02.492 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:02.492 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:02.492 INFO  Funcotator - Deflater: IntelDeflater
15:41:02.492 INFO  Funcotator - Inflater: IntelInflater
15:41:02.492 INFO  Funcotator - GCS max retries/reopens: 20
15:41:02.492 INFO  Funcotator - Requester pays: disabled
15:41:02.492 INFO  Funcotator - Initializing engine
15:41:02.493 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
15:41:02.493 INFO  Funcotator - Done initializing engine
15:41:02.493 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:02.493 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:02.493 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder14451555978199368974/TranscriptIdFile.txt
15:41:02.493 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:41:02.494 INFO  FuncotatorEngine - Transcript parsing complete.
15:41:02.494 INFO  Funcotator - Initializing data sources...
15:41:02.494 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:02.494 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:02.494 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
15:41:02.494 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
15:41:02.494 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
15:41:02.495 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
15:41:02.495 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
15:41:02.495 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
15:41:02.495 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
15:41:02.495 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
15:41:02.496 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
15:41:02.496 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
15:41:02.496 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
15:41:02.496 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
15:41:02.496 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
15:41:02.496 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
15:41:02.497 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
15:41:02.497 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:02.497 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
15:41:02.497 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
15:41:02.541 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
15:41:02.638 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
15:41:02.646 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
15:41:02.647 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
15:41:02.647 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
15:41:02.647 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
15:41:03.327 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
15:41:03.366 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
15:41:03.366 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:03.367 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
15:41:03.367 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
15:41:03.454 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:03.455 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:03.455 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
15:41:03.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:03.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:03.483 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
15:41:03.483 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
15:41:03.483 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
15:41:03.484 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:03.484 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
15:41:03.486 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
15:41:03.489 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
15:41:03.491 INFO  Funcotator - Initializing Funcotator Engine...
15:41:03.492 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:03.492 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:03.492 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.413048289240154331614.maf
15:41:03.492 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
15:41:03.494 INFO  ProgressMeter - Starting traversal
15:41:03.494 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:03.611 INFO  ProgressMeter -             unmapped              0.0                     4           2051.3
15:41:03.611 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:03.611 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:03.611 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2705326080
15:41:03.680 INFO  Funcotator - ------------------------------------------------------------
15:41:03.680 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:03.681 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:03.681 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:03.681 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:03.681 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:03 PM UTC
15:41:03.681 INFO  Funcotator - ------------------------------------------------------------
15:41:03.681 INFO  Funcotator - ------------------------------------------------------------
15:41:03.681 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:03.681 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:03.681 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:03.681 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:03.681 INFO  Funcotator - Deflater: IntelDeflater
15:41:03.681 INFO  Funcotator - Inflater: IntelInflater
15:41:03.681 INFO  Funcotator - GCS max retries/reopens: 20
15:41:03.681 INFO  Funcotator - Requester pays: disabled
15:41:03.681 INFO  Funcotator - Initializing engine
15:41:03.682 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
15:41:03.683 INFO  Funcotator - Done initializing engine
15:41:03.683 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:03.683 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:03.683 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder12747633791775546563/TranscriptIdFile.txt
15:41:03.683 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:41:03.683 INFO  FuncotatorEngine - Transcript parsing complete.
15:41:03.683 INFO  Funcotator - Initializing data sources...
15:41:03.683 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:03.683 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:03.683 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
15:41:03.684 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
15:41:03.684 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
15:41:03.684 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
15:41:03.684 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
15:41:03.684 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
15:41:03.685 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
15:41:03.685 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
15:41:03.685 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
15:41:03.685 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
15:41:03.685 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
15:41:03.686 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:03.686 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
15:41:03.686 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
15:41:03.686 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
15:41:03.686 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:03.686 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
15:41:03.687 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
15:41:03.732 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
15:41:03.751 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
15:41:03.829 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
15:41:03.830 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
15:41:03.830 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
15:41:03.830 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
15:41:04.429 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
15:41:04.468 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
15:41:04.468 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:04.469 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
15:41:04.470 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
15:41:04.554 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:04.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:04.555 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
15:41:04.582 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:04.582 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:04.583 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
15:41:04.583 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
15:41:04.584 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
15:41:04.584 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:04.584 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
15:41:04.586 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
15:41:04.589 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
15:41:04.591 INFO  Funcotator - Initializing Funcotator Engine...
15:41:04.591 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
15:41:04.592 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:04.592 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:04.592 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:04.592 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:04.592 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:04.593 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.37082038769372641513.maf
15:41:04.593 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
15:41:04.595 INFO  ProgressMeter - Starting traversal
15:41:04.595 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:04.623 INFO  ProgressMeter -             unmapped              0.0                     3           6428.6
15:41:04.623 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:04.624 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:04.624 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:04 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2705326080
15:41:04.695 INFO  Funcotator - ------------------------------------------------------------
15:41:04.695 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:04.695 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:04.695 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:04.695 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:04.695 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:04 PM UTC
15:41:04.695 INFO  Funcotator - ------------------------------------------------------------
15:41:04.695 INFO  Funcotator - ------------------------------------------------------------
15:41:04.695 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:04.695 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:04.695 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:04.695 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:04.695 INFO  Funcotator - Deflater: IntelDeflater
15:41:04.695 INFO  Funcotator - Inflater: IntelInflater
15:41:04.695 INFO  Funcotator - GCS max retries/reopens: 20
15:41:04.695 INFO  Funcotator - Requester pays: disabled
15:41:04.695 INFO  Funcotator - Initializing engine
15:41:04.696 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
15:41:04.697 INFO  Funcotator - Done initializing engine
15:41:04.697 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:04.697 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:04.697 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder904625633166475124/TranscriptIdFile.txt
15:41:04.697 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:41:04.697 INFO  FuncotatorEngine - Transcript parsing complete.
15:41:04.697 INFO  Funcotator - Initializing data sources...
15:41:04.697 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:04.697 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:04.697 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
15:41:04.698 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
15:41:04.698 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
15:41:04.698 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
15:41:04.698 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
15:41:04.698 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
15:41:04.699 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
15:41:04.699 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
15:41:04.699 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
15:41:04.699 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
15:41:04.699 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
15:41:04.699 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:04.700 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
15:41:04.700 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
15:41:04.700 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
15:41:04.700 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:04.700 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
15:41:04.701 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
15:41:04.744 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
15:41:04.763 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
15:41:04.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:04.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:04.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:41:04.771 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
15:41:05.416 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
15:41:05.454 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
15:41:05.454 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:05.455 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
15:41:05.456 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
15:41:05.537 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:05.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:05.538 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
15:41:05.566 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:05.566 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:05	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:05.567 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
15:41:05.567 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
15:41:05.567 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
15:41:05.567 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:05.568 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
15:41:05.570 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
15:41:05.573 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
15:41:05.575 INFO  Funcotator - Initializing Funcotator Engine...
15:41:05.575 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:05.575 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:05.575 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.413441557970666532976.maf
15:41:05.576 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
15:41:05.578 INFO  ProgressMeter - Starting traversal
15:41:05.578 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:05.694 INFO  ProgressMeter -             unmapped              0.0                     4           2069.0
15:41:05.694 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:05.695 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:05.695 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:05 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2705326080
15:41:05.771 INFO  Funcotator - ------------------------------------------------------------
15:41:05.772 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:05.772 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:05.772 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:05.772 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:05.772 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:05 PM UTC
15:41:05.772 INFO  Funcotator - ------------------------------------------------------------
15:41:05.772 INFO  Funcotator - ------------------------------------------------------------
15:41:05.772 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:05.772 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:05.772 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:05.772 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:05.772 INFO  Funcotator - Deflater: IntelDeflater
15:41:05.772 INFO  Funcotator - Inflater: IntelInflater
15:41:05.772 INFO  Funcotator - GCS max retries/reopens: 20
15:41:05.772 INFO  Funcotator - Requester pays: disabled
15:41:05.772 INFO  Funcotator - Initializing engine
15:41:05.774 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
15:41:05.775 INFO  Funcotator - Done initializing engine
15:41:05.775 INFO  Funcotator - Validating sequence dictionaries...
15:41:05.775 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:05.775 INFO  Funcotator - Initializing data sources...
15:41:05.776 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:05.776 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:05.776 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
15:41:05.776 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
15:41:05.776 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
15:41:05.776 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
15:41:05.777 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
15:41:05.777 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
15:41:05.777 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
15:41:05.777 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
15:41:05.777 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
15:41:05.778 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
15:41:05.778 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
15:41:05.778 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:05.778 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
15:41:05.778 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
15:41:05.778 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
15:41:05.778 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:05.778 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
15:41:05.779 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
15:41:05.821 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
15:41:05.840 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
15:41:05.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:05.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:05.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:41:05.849 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
15:41:06.587 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
15:41:06.626 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
15:41:06.626 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:06.627 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
15:41:06.627 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
15:41:06.709 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:06.710 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:06.710 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
15:41:06.738 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:06.738 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:06.738 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
15:41:06.739 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
15:41:06.739 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
15:41:06.739 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:06.740 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
15:41:06.742 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
15:41:06.745 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
15:41:06.747 INFO  Funcotator - Initializing Funcotator Engine...
15:41:06.747 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:06.747 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.
15:41:06.747 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator2005454779008821612.vcf
15:41:06.749 INFO  ProgressMeter - Starting traversal
15:41:06.749 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:09.020 INFO  ProgressMeter -             unmapped              0.0                   198           5231.2
15:41:09.020 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:09.020 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:09.030 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2990538752
15:41:09.031 WARN  gatk -   VCF Elapsed Time: 3.333546071s
15:41:09.031 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator2005454779008821612.vcf
15:41:09.034 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
15:41:09.110 INFO  Funcotator - ------------------------------------------------------------
15:41:09.110 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:09.110 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:09.110 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:09.110 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:09.110 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:09 PM UTC
15:41:09.110 INFO  Funcotator - ------------------------------------------------------------
15:41:09.110 INFO  Funcotator - ------------------------------------------------------------
15:41:09.110 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:09.110 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:09.110 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:09.110 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:09.110 INFO  Funcotator - Deflater: IntelDeflater
15:41:09.110 INFO  Funcotator - Inflater: IntelInflater
15:41:09.110 INFO  Funcotator - GCS max retries/reopens: 20
15:41:09.110 INFO  Funcotator - Requester pays: disabled
15:41:09.110 INFO  Funcotator - Initializing engine
15:41:09.112 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
15:41:09.114 INFO  Funcotator - Done initializing engine
15:41:09.114 INFO  Funcotator - Validating sequence dictionaries...
15:41:09.114 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:09.114 INFO  Funcotator - Initializing data sources...
15:41:09.114 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:09.114 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:09.115 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
15:41:09.115 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
15:41:09.115 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
15:41:09.115 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
15:41:09.115 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
15:41:09.116 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
15:41:09.116 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
15:41:09.116 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
15:41:09.116 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
15:41:09.116 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
15:41:09.116 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
15:41:09.116 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:09.117 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
15:41:09.117 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
15:41:09.117 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
15:41:09.117 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:09.117 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
15:41:09.118 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:41:09.161 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
15:41:09.180 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
15:41:09.187 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
15:41:09.187 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
15:41:09.187 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
15:41:09.188 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
15:41:09.783 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
15:41:09.820 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
15:41:09.820 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:09.821 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
15:41:09.821 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
15:41:09.901 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:09.901 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
15:41:09.902 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
15:41:09.929 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:09.929 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:09	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:09.930 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
15:41:09.930 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
15:41:09.930 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
15:41:09.930 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:09.931 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
15:41:09.933 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
15:41:09.936 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
15:41:09.939 INFO  Funcotator - Initializing Funcotator Engine...
15:41:09.940 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:09.940 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.
15:41:09.940 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator738854861749436499.maf
15:41:09.940 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
15:41:09.941 INFO  ProgressMeter - Starting traversal
15:41:09.941 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:12.147 INFO  ProgressMeter -             unmapped              0.0                   198           5385.3
15:41:12.147 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:12.147 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:12.147 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:12 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3061841920
15:41:12.148 WARN  gatk -   MAF Elapsed Time: 3.109984822s
15:41:12.223 INFO  Funcotator - ------------------------------------------------------------
15:41:12.223 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:12.223 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:12.223 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:12.223 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:12.223 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:12 PM UTC
15:41:12.223 INFO  Funcotator - ------------------------------------------------------------
15:41:12.223 INFO  Funcotator - ------------------------------------------------------------
15:41:12.223 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:12.223 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:12.223 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:12.223 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:12.223 INFO  Funcotator - Deflater: IntelDeflater
15:41:12.223 INFO  Funcotator - Inflater: IntelInflater
15:41:12.223 INFO  Funcotator - GCS max retries/reopens: 20
15:41:12.223 INFO  Funcotator - Requester pays: disabled
15:41:12.223 INFO  Funcotator - Initializing engine
15:41:12.225 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
15:41:12.227 INFO  Funcotator - Done initializing engine
15:41:12.227 INFO  Funcotator - Validating sequence dictionaries...
15:41:12.227 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:12.227 INFO  Funcotator - Initializing data sources...
15:41:12.227 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:12.227 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:12.227 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
15:41:12.227 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
15:41:12.228 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
15:41:12.228 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
15:41:12.228 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
15:41:12.228 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
15:41:12.228 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
15:41:12.228 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
15:41:12.229 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
15:41:12.229 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
15:41:12.229 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
15:41:12.229 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:12.229 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
15:41:12.229 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
15:41:12.230 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
15:41:12.230 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:12.230 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
15:41:12.230 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
15:41:12.273 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
15:41:12.292 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
15:41:12.344 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
15:41:12.344 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
15:41:12.345 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
15:41:12.345 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
15:41:12.928 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
15:41:12.967 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
15:41:12.967 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:12.968 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
15:41:12.968 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
15:41:13.050 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:13.051 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:13.051 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
15:41:13.078 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:13.079 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:13	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:13.079 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
15:41:13.079 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
15:41:13.080 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
15:41:13.080 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:13.081 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
15:41:13.084 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
15:41:13.087 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
15:41:13.089 INFO  Funcotator - Initializing Funcotator Engine...
15:41:13.090 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:13.090 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.
15:41:13.090 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator12603736747281401056.vcf
15:41:13.091 INFO  ProgressMeter - Starting traversal
15:41:13.091 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:14.129 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:41:14.129 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:41:14.944 INFO  ProgressMeter -             unmapped              0.0                   168           5439.8
15:41:14.944 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:41:14.945 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:41:14.951 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:14 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3061841920
15:41:14.951 WARN  gatk -   VCF Elapsed Time: 2.80141434s
15:41:14.952 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator12603736747281401056.vcf
15:41:14.954 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
15:41:15.030 INFO  Funcotator - ------------------------------------------------------------
15:41:15.030 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:15.030 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:15.030 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:15.030 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:15.030 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:15 PM UTC
15:41:15.030 INFO  Funcotator - ------------------------------------------------------------
15:41:15.030 INFO  Funcotator - ------------------------------------------------------------
15:41:15.030 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:15.030 INFO  Funcotator - Deflater: IntelDeflater
15:41:15.030 INFO  Funcotator - Inflater: IntelInflater
15:41:15.030 INFO  Funcotator - GCS max retries/reopens: 20
15:41:15.030 INFO  Funcotator - Requester pays: disabled
15:41:15.030 INFO  Funcotator - Initializing engine
15:41:15.033 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
15:41:15.033 INFO  Funcotator - Done initializing engine
15:41:15.034 INFO  Funcotator - Validating sequence dictionaries...
15:41:15.034 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:15.034 INFO  Funcotator - Initializing data sources...
15:41:15.034 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:15.034 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:15.034 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
15:41:15.034 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
15:41:15.035 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
15:41:15.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:15.035 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
15:41:15.035 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
15:41:15.035 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
15:41:15.036 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
15:41:15.036 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
15:41:15.036 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
15:41:15.036 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
15:41:15.036 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:15.036 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
15:41:15.037 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
15:41:15.037 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
15:41:15.037 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:15.037 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
15:41:15.037 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
15:41:15.094 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
15:41:15.113 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
15:41:15.120 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
15:41:15.120 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
15:41:15.121 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
15:41:15.121 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
15:41:15.761 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
15:41:15.802 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
15:41:15.802 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:15.803 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
15:41:15.803 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
15:41:15.886 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:15.887 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:15.887 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
15:41:15.915 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:15.915 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:15.915 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
15:41:15.916 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
15:41:15.916 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
15:41:15.916 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:15.917 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
15:41:15.919 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
15:41:15.922 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
15:41:15.925 INFO  Funcotator - Initializing Funcotator Engine...
15:41:15.926 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:15.926 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.
15:41:15.926 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator2744604888854708202.maf
15:41:15.926 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
15:41:15.928 INFO  ProgressMeter - Starting traversal
15:41:15.928 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:16.974 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:41:16.974 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:41:17.788 INFO  ProgressMeter -             unmapped              0.0                   168           5419.4
15:41:17.788 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:41:17.788 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:41:17.789 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:17 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3087007744
15:41:17.789 WARN  gatk -   MAF Elapsed Time: 2.831328071s
15:41:17.863 INFO  Funcotator - ------------------------------------------------------------
15:41:17.863 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:17.863 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:17.863 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:17.863 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:17.863 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:17 PM UTC
15:41:17.863 INFO  Funcotator - ------------------------------------------------------------
15:41:17.863 INFO  Funcotator - ------------------------------------------------------------
15:41:17.863 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:17.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:17.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:17.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:17.863 INFO  Funcotator - Deflater: IntelDeflater
15:41:17.863 INFO  Funcotator - Inflater: IntelInflater
15:41:17.863 INFO  Funcotator - GCS max retries/reopens: 20
15:41:17.863 INFO  Funcotator - Requester pays: disabled
15:41:17.863 INFO  Funcotator - Initializing engine
15:41:17.866 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
15:41:17.867 INFO  Funcotator - Done initializing engine
15:41:17.867 INFO  Funcotator - Validating sequence dictionaries...
15:41:17.867 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:17.867 INFO  Funcotator - Initializing data sources...
15:41:17.867 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:17.867 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:17.868 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
15:41:17.868 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
15:41:17.868 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
15:41:17.868 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
15:41:17.868 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
15:41:17.868 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
15:41:17.869 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
15:41:17.869 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
15:41:17.869 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
15:41:17.869 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
15:41:17.869 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
15:41:17.869 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
15:41:17.870 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
15:41:17.870 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
15:41:17.870 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
15:41:17.870 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:17.870 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
15:41:17.870 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
15:41:17.914 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
15:41:17.933 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
15:41:17.941 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
15:41:17.941 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
15:41:17.941 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
15:41:17.942 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
15:41:18.573 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
15:41:18.611 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
15:41:18.611 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:18.612 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
15:41:18.612 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
15:41:18.707 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:18.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:18.708 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
15:41:18.735 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:18.736 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:18.736 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
15:41:18.736 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
15:41:18.737 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
15:41:18.737 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:18.738 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
15:41:18.740 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
15:41:18.742 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
15:41:18.745 INFO  Funcotator - Initializing Funcotator Engine...
15:41:18.745 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:18.745 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.
15:41:18.745 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator4745312538963812989.vcf
15:41:18.746 INFO  ProgressMeter - Starting traversal
15:41:18.746 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:18.756 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
15:41:18.757 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:41:18.757 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:18.758 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:18 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3087007744
15:41:18.758 WARN  gatk -   VCF Elapsed Time: 0.966951116s
15:41:18.759 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator4745312538963812989.vcf
15:41:18.760 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
15:41:18.832 INFO  Funcotator - ------------------------------------------------------------
15:41:18.832 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:18.832 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:18.832 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:18.832 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:18.832 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:18 PM UTC
15:41:18.832 INFO  Funcotator - ------------------------------------------------------------
15:41:18.832 INFO  Funcotator - ------------------------------------------------------------
15:41:18.832 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:18.832 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:18.832 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:18.832 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:18.832 INFO  Funcotator - Deflater: IntelDeflater
15:41:18.832 INFO  Funcotator - Inflater: IntelInflater
15:41:18.832 INFO  Funcotator - GCS max retries/reopens: 20
15:41:18.832 INFO  Funcotator - Requester pays: disabled
15:41:18.833 INFO  Funcotator - Initializing engine
15:41:18.835 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
15:41:18.836 INFO  Funcotator - Done initializing engine
15:41:18.836 INFO  Funcotator - Validating sequence dictionaries...
15:41:18.836 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:18.836 INFO  Funcotator - Initializing data sources...
15:41:18.836 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:18.836 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:18.836 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
15:41:18.836 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
15:41:18.837 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:41:18.837 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
15:41:18.837 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
15:41:18.837 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
15:41:18.837 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
15:41:18.838 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
15:41:18.838 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
15:41:18.838 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
15:41:18.838 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
15:41:18.838 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
15:41:18.838 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
15:41:18.839 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
15:41:18.839 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
15:41:18.839 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:18.839 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
15:41:18.839 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
15:41:18.882 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
15:41:18.952 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
15:41:18.959 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
15:41:18.960 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
15:41:18.960 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
15:41:18.960 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
15:41:19.621 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
15:41:19.660 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
15:41:19.660 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:19.661 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
15:41:19.662 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
15:41:19.744 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:19.744 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
15:41:19.745 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
15:41:19.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:19.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:19	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:19.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:41:19.773 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
15:41:19.773 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
15:41:19.773 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:19.774 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
15:41:19.776 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
15:41:19.779 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
15:41:19.781 INFO  Funcotator - Initializing Funcotator Engine...
15:41:19.781 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:19.781 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.
15:41:19.781 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator8492132355201321119.maf
15:41:19.781 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
15:41:19.782 INFO  ProgressMeter - Starting traversal
15:41:19.782 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:19.794 INFO  ProgressMeter -             unmapped              0.0                     1           5000.0
15:41:19.794 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:41:19.794 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:19.794 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:19 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3087007744
15:41:19.794 WARN  gatk -   MAF Elapsed Time: 1.033744621s
15:41:19.863 INFO  Funcotator - ------------------------------------------------------------
15:41:19.863 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:19.863 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:19.863 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:19.863 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:19.863 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:19 PM UTC
15:41:19.863 INFO  Funcotator - ------------------------------------------------------------
15:41:19.863 INFO  Funcotator - ------------------------------------------------------------
15:41:19.863 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:19.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:19.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:19.863 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:19.863 INFO  Funcotator - Deflater: IntelDeflater
15:41:19.863 INFO  Funcotator - Inflater: IntelInflater
15:41:19.863 INFO  Funcotator - GCS max retries/reopens: 20
15:41:19.863 INFO  Funcotator - Requester pays: disabled
15:41:19.863 INFO  Funcotator - Initializing engine
15:41:19.892 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
15:41:19.915 INFO  Funcotator - Done initializing engine
15:41:19.915 INFO  Funcotator - Validating sequence dictionaries...
15:41:19.922 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:19.922 INFO  Funcotator - Initializing data sources...
15:41:19.922 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:19.922 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:19.922 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
15:41:19.922 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
15:41:19.923 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/hg38/cosmic_tissue.tsv
15:41:19.923 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
15:41:19.923 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
15:41:19.923 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
15:41:19.923 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
15:41:19.924 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
15:41:19.924 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
15:41:19.924 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
15:41:19.924 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/hg38/achilles_lineage_results.import.txt
15:41:19.924 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
15:41:19.924 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
15:41:19.925 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:19.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
15:41:19.966 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
15:41:19.984 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
15:41:19.991 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
15:41:19.991 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
15:41:19.991 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
15:41:19.992 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
15:41:20.716 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
15:41:20.781 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
15:41:20.782 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:20.782 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
15:41:20.783 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
15:41:20.784 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
15:41:20.784 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
15:41:20.785 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
15:41:20.785 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:20.785 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
15:41:20.786 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
15:41:20.788 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
15:41:20.790 INFO  Funcotator - Initializing Funcotator Engine...
15:41:20.793 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:20.793 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator3910627379515640329.vcf
15:41:20.806 INFO  ProgressMeter - Starting traversal
15:41:20.806 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:20.833 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.
15:41:20.835 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:41:20.838 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:20.841 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:20.841 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:20.842 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:20.842 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:20.842 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:20.843 INFO  ProgressMeter -             unmapped              0.0                     5           8108.1
15:41:20.843 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:41:20.843 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:20.855 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:20 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3219128320
15:41:20.855 WARN  gatk -   VCF Elapsed Time: 1.059806493s
15:41:20.855 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator3910627379515640329.vcf
15:41:20.888 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
15:41:20.967 INFO  Funcotator - ------------------------------------------------------------
15:41:20.967 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:20.967 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:20.967 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:20.967 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:20.967 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:20 PM UTC
15:41:20.967 INFO  Funcotator - ------------------------------------------------------------
15:41:20.967 INFO  Funcotator - ------------------------------------------------------------
15:41:20.967 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:20.967 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:20.967 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:20.967 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:20.967 INFO  Funcotator - Deflater: IntelDeflater
15:41:20.967 INFO  Funcotator - Inflater: IntelInflater
15:41:20.967 INFO  Funcotator - GCS max retries/reopens: 20
15:41:20.967 INFO  Funcotator - Requester pays: disabled
15:41:20.967 INFO  Funcotator - Initializing engine
15:41:20.998 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
15:41:21.030 INFO  Funcotator - Done initializing engine
15:41:21.030 INFO  Funcotator - Validating sequence dictionaries...
15:41:21.038 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:21.038 INFO  Funcotator - Initializing data sources...
15:41:21.038 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:21.038 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:21.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
15:41:21.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
15:41:21.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
15:41:21.039 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
15:41:21.039 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
15:41:21.040 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
15:41:21.040 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
15:41:21.040 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
15:41:21.040 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
15:41:21.040 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
15:41:21.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
15:41:21.041 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:41:21.041 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
15:41:21.041 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:21.041 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
15:41:21.084 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
15:41:21.104 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
15:41:21.111 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/hg38/Familial_Cancer_Genes.no_dupes.tsv
15:41:21.111 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
15:41:21.111 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
15:41:21.112 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
15:41:21.709 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
15:41:21.775 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
15:41:21.775 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:21.776 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
15:41:21.776 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
15:41:21.777 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
15:41:21.778 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
15:41:21.778 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
15:41:21.778 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:21.779 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
15:41:21.780 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
15:41:21.782 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
15:41:21.783 INFO  Funcotator - Initializing Funcotator Engine...
15:41:21.787 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:21.787 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator1937100518754839419.maf
15:41:21.789 INFO  ProgressMeter - Starting traversal
15:41:21.789 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:21.811 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.
15:41:21.811 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:41:21.813 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:21.816 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:21.816 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:41:21.817 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:21.817 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:21.817 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:41:21.818 INFO  ProgressMeter -             unmapped              0.0                     5          10344.8
15:41:21.818 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:41:21.818 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:21.818 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:21 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3219128320
15:41:21.818 WARN  gatk -   MAF Elapsed Time: 0.922016984s
15:41:21.892 INFO  Funcotator - ------------------------------------------------------------
15:41:21.892 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:21.892 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:21.892 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:21.892 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:21.892 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:21 PM UTC
15:41:21.892 INFO  Funcotator - ------------------------------------------------------------
15:41:21.892 INFO  Funcotator - ------------------------------------------------------------
15:41:21.892 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:21.892 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:21.892 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:21.892 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:21.892 INFO  Funcotator - Deflater: IntelDeflater
15:41:21.892 INFO  Funcotator - Inflater: IntelInflater
15:41:21.892 INFO  Funcotator - GCS max retries/reopens: 20
15:41:21.892 INFO  Funcotator - Requester pays: disabled
15:41:21.892 INFO  Funcotator - Initializing engine
15:41:21.895 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
15:41:21.896 INFO  Funcotator - Done initializing engine
15:41:21.896 INFO  Funcotator - Validating sequence dictionaries...
15:41:21.896 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:21.896 INFO  Funcotator - Initializing data sources...
15:41:21.896 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:21.896 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:21.897 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
15:41:21.897 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
15:41:21.897 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
15:41:21.897 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
15:41:21.897 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
15:41:21.898 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:21.898 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
15:41:21.898 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
15:41:21.898 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
15:41:21.898 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
15:41:21.898 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
15:41:21.899 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:21.899 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
15:41:21.899 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
15:41:21.899 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
15:41:21.899 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:21.899 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
15:41:21.900 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
15:41:21.942 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
15:41:21.961 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
15:41:21.968 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
15:41:21.969 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
15:41:21.969 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
15:41:21.969 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
15:41:22.573 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
15:41:22.612 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
15:41:22.612 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:22.613 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
15:41:22.613 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
15:41:22.696 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:22.696 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:22.697 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
15:41:22.724 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:22.724 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:22	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:22.725 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
15:41:22.725 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
15:41:22.726 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
15:41:22.726 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:22.726 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
15:41:22.728 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
15:41:22.731 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
15:41:22.733 INFO  Funcotator - Initializing Funcotator Engine...
15:41:22.734 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:22.734 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.
15:41:22.734 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator6767625029833761716.vcf
15:41:22.737 INFO  ProgressMeter - Starting traversal
15:41:22.737 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:28.334 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:41:28.334 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:41:28.335 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16152.2
15:41:28.335 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:41:28.335 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:41:28.358 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3219128320
15:41:28.358 WARN  gatk -   VCF Elapsed Time: 6.538590876s
15:41:28.359 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator6767625029833761716.vcf
15:41:28.367 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
15:41:28.456 INFO  Funcotator - ------------------------------------------------------------
15:41:28.456 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:28.456 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:28.456 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:28.456 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:28.456 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:28 PM UTC
15:41:28.456 INFO  Funcotator - ------------------------------------------------------------
15:41:28.456 INFO  Funcotator - ------------------------------------------------------------
15:41:28.456 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:28.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:28.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:28.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:28.456 INFO  Funcotator - Deflater: IntelDeflater
15:41:28.456 INFO  Funcotator - Inflater: IntelInflater
15:41:28.456 INFO  Funcotator - GCS max retries/reopens: 20
15:41:28.456 INFO  Funcotator - Requester pays: disabled
15:41:28.456 INFO  Funcotator - Initializing engine
15:41:28.458 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
15:41:28.460 INFO  Funcotator - Done initializing engine
15:41:28.460 INFO  Funcotator - Validating sequence dictionaries...
15:41:28.460 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:28.460 INFO  Funcotator - Initializing data sources...
15:41:28.460 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:28.460 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:28.460 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
15:41:28.460 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
15:41:28.461 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:41:28.461 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:28.461 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
15:41:28.461 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
15:41:28.461 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
15:41:28.461 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
15:41:28.462 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
15:41:28.462 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
15:41:28.462 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
15:41:28.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:28.462 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
15:41:28.462 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
15:41:28.463 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
15:41:28.463 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:28.463 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
15:41:28.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:41:28.505 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:41:28.524 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:28.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:28.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:28.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:41:28.532 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
15:41:29.131 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
15:41:29.170 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
15:41:29.170 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:29.171 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
15:41:29.171 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
15:41:29.256 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:29.256 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:29.257 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
15:41:29.285 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:29.285 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:29.285 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
15:41:29.286 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
15:41:29.286 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
15:41:29.286 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:29.287 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
15:41:29.289 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
15:41:29.292 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
15:41:29.294 INFO  Funcotator - Initializing Funcotator Engine...
15:41:29.294 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:29.294 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.
15:41:29.294 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator8041170745282413629.maf
15:41:29.294 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
15:41:29.295 INFO  ProgressMeter - Starting traversal
15:41:29.295 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:34.587 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:41:34.588 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:41:34.588 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17082.9
15:41:34.588 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:41:34.588 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:41:34.589 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:34 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3219128320
15:41:34.589 WARN  gatk -   MAF Elapsed Time: 6.202396895s
15:41:34.670 INFO  Funcotator - ------------------------------------------------------------
15:41:34.670 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:34.670 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:34.671 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:34.671 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:34.671 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:34 PM UTC
15:41:34.671 INFO  Funcotator - ------------------------------------------------------------
15:41:34.671 INFO  Funcotator - ------------------------------------------------------------
15:41:34.671 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:34.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:34.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:34.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:34.671 INFO  Funcotator - Deflater: IntelDeflater
15:41:34.671 INFO  Funcotator - Inflater: IntelInflater
15:41:34.671 INFO  Funcotator - GCS max retries/reopens: 20
15:41:34.671 INFO  Funcotator - Requester pays: disabled
15:41:34.671 INFO  Funcotator - Initializing engine
15:41:34.673 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
15:41:34.674 INFO  Funcotator - Done initializing engine
15:41:34.674 INFO  Funcotator - Validating sequence dictionaries...
15:41:34.674 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:34.674 INFO  Funcotator - Initializing data sources...
15:41:34.674 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:34.674 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:34.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:41:34.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:41:34.675 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
15:41:34.675 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
15:41:34.675 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
15:41:34.675 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
15:41:34.675 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
15:41:34.675 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
15:41:34.676 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
15:41:34.676 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
15:41:34.676 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
15:41:34.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:34.676 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
15:41:34.676 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
15:41:34.676 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
15:41:34.676 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:34.676 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
15:41:34.677 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
15:41:34.743 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
15:41:34.762 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:34.769 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
15:41:34.769 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
15:41:34.769 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
15:41:34.770 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
15:41:35.369 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
15:41:35.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:41:35.408 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:35.409 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
15:41:35.409 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
15:41:35.491 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:35.491 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:35.492 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
15:41:35.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:35.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:35.519 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
15:41:35.520 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
15:41:35.520 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
15:41:35.520 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:35.521 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
15:41:35.523 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
15:41:35.526 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
15:41:35.528 INFO  Funcotator - Initializing Funcotator Engine...
15:41:35.528 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:35.528 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.
15:41:35.528 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator9709081144685250418.vcf
15:41:35.529 INFO  ProgressMeter - Starting traversal
15:41:35.529 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:37.547 INFO  ProgressMeter -             unmapped              0.0                   198           5887.0
15:41:37.547 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:37.547 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:37.557 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3219128320
15:41:37.628 INFO  Funcotator - ------------------------------------------------------------
15:41:37.628 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:37.628 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:37.628 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:37.628 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:37.628 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:37 PM UTC
15:41:37.628 INFO  Funcotator - ------------------------------------------------------------
15:41:37.628 INFO  Funcotator - ------------------------------------------------------------
15:41:37.628 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:37.628 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:37.628 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:37.628 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:37.628 INFO  Funcotator - Deflater: IntelDeflater
15:41:37.628 INFO  Funcotator - Inflater: IntelInflater
15:41:37.628 INFO  Funcotator - GCS max retries/reopens: 20
15:41:37.628 INFO  Funcotator - Requester pays: disabled
15:41:37.628 INFO  Funcotator - Initializing engine
15:41:37.631 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
15:41:37.632 INFO  Funcotator - Done initializing engine
15:41:37.632 INFO  Funcotator - Validating sequence dictionaries...
15:41:37.632 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:37.632 INFO  Funcotator - Initializing data sources...
15:41:37.632 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:37.632 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:37.632 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
15:41:37.633 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
15:41:37.633 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
15:41:37.633 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
15:41:37.633 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
15:41:37.633 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
15:41:37.633 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
15:41:37.634 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
15:41:37.634 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
15:41:37.634 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
15:41:37.634 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
15:41:37.634 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:37.634 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
15:41:37.635 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
15:41:37.635 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:37.635 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:37.635 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
15:41:37.635 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
15:41:37.678 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
15:41:37.696 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
15:41:37.704 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
15:41:37.704 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
15:41:37.704 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
15:41:37.705 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
15:41:38.341 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
15:41:38.380 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:41:38.380 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:38.381 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
15:41:38.381 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:41:38.463 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:38.464 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
15:41:38.464 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
15:41:38.491 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:38.492 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:38.492 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
15:41:38.493 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
15:41:38.493 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
15:41:38.493 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:38.494 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
15:41:38.496 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
15:41:38.499 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
15:41:38.501 INFO  Funcotator - Initializing Funcotator Engine...
15:41:38.501 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:38.501 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.
15:41:38.501 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator13982721782830688576.maf
15:41:38.501 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
15:41:38.502 INFO  ProgressMeter - Starting traversal
15:41:38.502 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:40.488 INFO  ProgressMeter -             unmapped              0.0                   198           5981.9
15:41:40.488 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:40.488 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:40.488 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3238002688
15:41:40.558 INFO  Funcotator - ------------------------------------------------------------
15:41:40.558 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:40.558 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:40.558 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:40.558 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:40.558 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:40 PM UTC
15:41:40.558 INFO  Funcotator - ------------------------------------------------------------
15:41:40.558 INFO  Funcotator - ------------------------------------------------------------
15:41:40.558 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:40.558 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:40.558 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:40.558 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:40.558 INFO  Funcotator - Deflater: IntelDeflater
15:41:40.558 INFO  Funcotator - Inflater: IntelInflater
15:41:40.558 INFO  Funcotator - GCS max retries/reopens: 20
15:41:40.558 INFO  Funcotator - Requester pays: disabled
15:41:40.558 INFO  Funcotator - Initializing engine
15:41:40.560 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
15:41:40.561 INFO  Funcotator - Done initializing engine
15:41:40.561 INFO  Funcotator - Validating sequence dictionaries...
15:41:40.561 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:40.561 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3238002688
15:41:40.625 INFO  Funcotator - ------------------------------------------------------------
15:41:40.625 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:40.625 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:40.625 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:40.625 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:40.625 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:40 PM UTC
15:41:40.625 INFO  Funcotator - ------------------------------------------------------------
15:41:40.625 INFO  Funcotator - ------------------------------------------------------------
15:41:40.625 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:40.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:40.626 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:40.626 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:40.626 INFO  Funcotator - Deflater: IntelDeflater
15:41:40.626 INFO  Funcotator - Inflater: IntelInflater
15:41:40.626 INFO  Funcotator - GCS max retries/reopens: 20
15:41:40.626 INFO  Funcotator - Requester pays: disabled
15:41:40.626 INFO  Funcotator - Initializing engine
15:41:40.627 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
15:41:40.644 INFO  Funcotator - Done initializing engine
15:41:40.645 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:40.645 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:40.645 INFO  Funcotator - Initializing data sources...
15:41:40.645 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:40.645 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:40.645 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
15:41:40.645 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
15:41:40.645 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
15:41:40.645 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:40.645 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
15:41:40.645 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:40.646 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
15:41:40.646 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
15:41:40.647 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
15:41:40.647 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:40.647 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/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:40.655 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
15:41:40.664 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
15:41:40.672 INFO  Funcotator - Initializing Funcotator Engine...
15:41:40.677 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:40.677 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13588040595389638571.vcf
15:41:40.689 INFO  ProgressMeter - Starting traversal
15:41:40.689 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:40.717 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
15:41:40.717 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:41:40.717 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:41:40.723 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3238002688
15:41:40.724 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13588040595389638571.vcf
15:41:40.803 INFO  Funcotator - ------------------------------------------------------------
15:41:40.803 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:40.803 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:40.803 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:40.803 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:40.803 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:40 PM UTC
15:41:40.803 INFO  Funcotator - ------------------------------------------------------------
15:41:40.803 INFO  Funcotator - ------------------------------------------------------------
15:41:40.803 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:40.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:40.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:40.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:40.803 INFO  Funcotator - Deflater: IntelDeflater
15:41:40.803 INFO  Funcotator - Inflater: IntelInflater
15:41:40.803 INFO  Funcotator - GCS max retries/reopens: 20
15:41:40.803 INFO  Funcotator - Requester pays: disabled
15:41:40.803 INFO  Funcotator - Initializing engine
15:41:40.804 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
15:41:40.806 INFO  Funcotator - Done initializing engine
15:41:40.806 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:40.806 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:40.806 INFO  Funcotator - Initializing data sources...
15:41:40.806 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:40.806 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:40.806 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
15:41:40.806 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
15:41:40.806 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
15:41:40.807 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:40.807 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
15:41:40.807 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:40.807 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
15:41:40.807 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
15:41:40.808 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
15:41:40.808 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:40.808 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
15:41:40.809 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
15:41:40.810 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
15:41:40.811 INFO  Funcotator - Initializing Funcotator Engine...
15:41:40.811 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:40.811 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.
15:41:40.811 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13207620149183664428.vcf
15:41:40.819 INFO  ProgressMeter - Starting traversal
15:41:40.819 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:40.828 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:41:40.828 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:41:40.828 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:41:40.831 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3238002688
15:41:40.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13207620149183664428.vcf
15:41:40.900 INFO  Funcotator - ------------------------------------------------------------
15:41:40.900 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:40.900 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:40.900 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:40.900 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:40.900 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:40 PM UTC
15:41:40.900 INFO  Funcotator - ------------------------------------------------------------
15:41:40.900 INFO  Funcotator - ------------------------------------------------------------
15:41:40.900 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:40.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:40.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:40.900 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:40.900 INFO  Funcotator - Deflater: IntelDeflater
15:41:40.900 INFO  Funcotator - Inflater: IntelInflater
15:41:40.900 INFO  Funcotator - GCS max retries/reopens: 20
15:41:40.900 INFO  Funcotator - Requester pays: disabled
15:41:40.900 INFO  Funcotator - Initializing engine
15:41:40.901 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
15:41:40.913 INFO  Funcotator - Done initializing engine
15:41:40.913 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:40.913 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:40.913 INFO  Funcotator - Initializing data sources...
15:41:40.913 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:40.913 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:40.914 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
15:41:40.914 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
15:41:40.914 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
15:41:40.914 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:40.914 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
15:41:40.914 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:40.915 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
15:41:40.915 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
15:41:40.915 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
15:41:40.915 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:40.916 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
15:41:40.924 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
15:41:40.933 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
15:41:40.941 INFO  Funcotator - Initializing Funcotator Engine...
15:41:40.945 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:40.945 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3192160244778431638.vcf
15:41:40.956 INFO  ProgressMeter - Starting traversal
15:41:40.956 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:40.961 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)
15:41:40.962 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)
15:41:40.962 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.962 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:40.962 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:41:40.962 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:41:40.964 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.964 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:40.964 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:41:40.965 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:41:40.965 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)
15:41:40.965 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)
15:41:40.965 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.966 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:40.966 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:41:40.966 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:41:40.966 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)
15:41:40.967 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)
15:41:40.967 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:41:40.967 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:41:40.967 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:41:40.967 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:41:40.968 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.968 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:40.968 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:41:40.968 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:41:40.969 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.969 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:40.969 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:41:40.969 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:41:40.970 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)
15:41:40.970 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)
15:41:40.970 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:41:40.970 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:40.971 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:41:40.971 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:41:40.971 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)
15:41:40.971 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)
15:41:40.971 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.972 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:40.972 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:41:40.972 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:41:40.973 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:41:40.973 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:40.973 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:41:40.973 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:41:40.973 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)
15:41:40.974 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)
15:41:40.974 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:40.974 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:40.974 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:41:40.974 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:41:40.975 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
15:41:40.975 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:41:40.975 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:40.980 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:40 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3238002688
15:41:40.981 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3192160244778431638.vcf
15:41:41.055 INFO  Funcotator - ------------------------------------------------------------
15:41:41.055 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:41.055 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:41.055 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:41.055 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:41.055 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:41 PM UTC
15:41:41.055 INFO  Funcotator - ------------------------------------------------------------
15:41:41.055 INFO  Funcotator - ------------------------------------------------------------
15:41:41.055 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:41.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:41.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:41.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:41.055 INFO  Funcotator - Deflater: IntelDeflater
15:41:41.055 INFO  Funcotator - Inflater: IntelInflater
15:41:41.055 INFO  Funcotator - GCS max retries/reopens: 20
15:41:41.055 INFO  Funcotator - Requester pays: disabled
15:41:41.055 INFO  Funcotator - Initializing engine
15:41:41.057 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
15:41:41.059 INFO  Funcotator - Done initializing engine
15:41:41.059 INFO  Funcotator - Validating sequence dictionaries...
15:41:41.059 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:41.059 INFO  Funcotator - Initializing data sources...
15:41:41.059 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:41.059 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:41.059 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
15:41:41.059 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
15:41:41.060 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
15:41:41.060 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
15:41:41.060 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
15:41:41.060 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
15:41:41.060 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
15:41:41.061 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
15:41:41.061 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
15:41:41.061 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
15:41:41.061 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
15:41:41.061 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:41.061 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
15:41:41.062 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
15:41:41.062 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
15:41:41.062 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:41.062 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
15:41:41.062 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
15:41:41.107 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
15:41:41.126 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
15:41:41.133 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
15:41:41.133 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
15:41:41.133 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
15:41:41.134 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
15:41:41.742 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
15:41:41.779 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
15:41:41.779 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:41.780 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
15:41:41.781 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
15:41:41.871 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:41.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:41.872 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
15:41:41.899 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:41.899 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:41	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:41.900 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
15:41:41.900 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
15:41:41.901 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
15:41:41.901 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:41.901 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
15:41:41.903 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
15:41:41.906 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
15:41:41.908 INFO  Funcotator - Initializing Funcotator Engine...
15:41:41.908 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:41.908 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.
15:41:41.908 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator10505776916546756937.vcf
15:41:41.912 INFO  ProgressMeter - Starting traversal
15:41:41.912 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:41.998 INFO  ProgressMeter -             unmapped              0.0                     1            697.7
15:41:41.998 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:41:41.999 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:41.999 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:41 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3238002688
15:41:42.000 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator10505776916546756937.vcf
15:41:42.068 INFO  Funcotator - ------------------------------------------------------------
15:41:42.068 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:42.068 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:42.068 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:42.068 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:42.068 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:42 PM UTC
15:41:42.068 INFO  Funcotator - ------------------------------------------------------------
15:41:42.068 INFO  Funcotator - ------------------------------------------------------------
15:41:42.068 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:42.068 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:42.068 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:42.068 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:42.068 INFO  Funcotator - Deflater: IntelDeflater
15:41:42.068 INFO  Funcotator - Inflater: IntelInflater
15:41:42.068 INFO  Funcotator - GCS max retries/reopens: 20
15:41:42.068 INFO  Funcotator - Requester pays: disabled
15:41:42.068 INFO  Funcotator - Initializing engine
15:41:42.071 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
15:41:42.072 INFO  Funcotator - Done initializing engine
15:41:42.072 INFO  Funcotator - Validating sequence dictionaries...
15:41:42.072 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:42.072 INFO  Funcotator - Initializing data sources...
15:41:42.072 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:42.072 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:42.073 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
15:41:42.073 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
15:41:42.073 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
15:41:42.073 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
15:41:42.073 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
15:41:42.074 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
15:41:42.074 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
15:41:42.074 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
15:41:42.074 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
15:41:42.074 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
15:41:42.074 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
15:41:42.075 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:42.075 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
15:41:42.075 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
15:41:42.075 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
15:41:42.075 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:42.075 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
15:41:42.076 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
15:41:42.120 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
15:41:42.138 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
15:41:42.145 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
15:41:42.146 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
15:41:42.146 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
15:41:42.146 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
15:41:42.816 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
15:41:42.855 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
15:41:42.855 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:42.855 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
15:41:42.856 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
15:41:42.937 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:42.938 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:42.938 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
15:41:42.984 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
15:41:42.984 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
WARNING	2025-05-27 15:41:42	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:42.985 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
15:41:42.985 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
15:41:42.986 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
15:41:42.986 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:42.987 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
15:41:42.990 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:42.994 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
15:41:42.998 INFO  Funcotator - Initializing Funcotator Engine...
15:41:42.998 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:42.998 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.
15:41:42.998 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator759209184127485144.vcf
15:41:43.004 INFO  ProgressMeter - Starting traversal
15:41:43.004 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:43.014 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:41:43.055 INFO  ProgressMeter -             unmapped              0.0                     2           2352.9
15:41:43.055 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:41:43.055 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:43.056 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3300917248
15:41:43.057 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator759209184127485144.vcf
15:41:43.126 INFO  Funcotator - ------------------------------------------------------------
15:41:43.126 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:43.126 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:43.126 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:43.126 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:43.126 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:43 PM UTC
15:41:43.126 INFO  Funcotator - ------------------------------------------------------------
15:41:43.126 INFO  Funcotator - ------------------------------------------------------------
15:41:43.126 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:43.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:43.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:43.126 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:43.126 INFO  Funcotator - Deflater: IntelDeflater
15:41:43.126 INFO  Funcotator - Inflater: IntelInflater
15:41:43.126 INFO  Funcotator - GCS max retries/reopens: 20
15:41:43.126 INFO  Funcotator - Requester pays: disabled
15:41:43.126 INFO  Funcotator - Initializing engine
15:41:43.128 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
15:41:43.129 INFO  Funcotator - Done initializing engine
15:41:43.129 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:43.129 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:43.129 INFO  Funcotator - Initializing data sources...
15:41:43.129 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:43.129 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:43.130 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
15:41:43.130 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
15:41:43.130 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
15:41:43.130 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
15:41:43.130 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
15:41:43.130 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
15:41:43.131 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
15:41:43.131 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
15:41:43.131 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
15:41:43.131 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
15:41:43.131 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:41:43.131 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:43.132 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
15:41:43.132 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
15:41:43.132 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
15:41:43.132 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:43.132 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
15:41:43.132 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
15:41:43.176 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
15:41:43.243 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
15:41:43.250 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
15:41:43.251 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
15:41:43.251 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
15:41:43.251 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
15:41:43.930 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
15:41:43.969 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
15:41:43.969 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:43.970 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
15:41:43.970 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
15:41:44.051 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:44.052 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:44.052 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
15:41:44.079 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:44.079 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:44.080 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
15:41:44.080 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
15:41:44.080 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
15:41:44.081 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:44.081 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
15:41:44.083 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
15:41:44.086 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
15:41:44.088 INFO  Funcotator - Initializing Funcotator Engine...
15:41:44.088 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:44.088 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.
15:41:44.088 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
15:41:44.088 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
15:41:44.088 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
15:41:44.088 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6283801833601431003.vcf
15:41:44.092 INFO  ProgressMeter - Starting traversal
15:41:44.092 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:44.126 INFO  ProgressMeter -             unmapped              0.0                     1           1764.7
15:41:44.126 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:41:44.126 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:44.127 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3376414720
15:41:44.127 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6283801833601431003.vcf
15:41:44.129 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_expected_out.vcf
[May 27, 2025 at 3:41:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
[May 27, 2025 at 3:41:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:44.380 INFO  Funcotator - ------------------------------------------------------------
15:41:44.380 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:44.380 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:44.380 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:44.380 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:44.380 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:44 PM UTC
15:41:44.380 INFO  Funcotator - ------------------------------------------------------------
15:41:44.380 INFO  Funcotator - ------------------------------------------------------------
15:41:44.380 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:44.380 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:44.380 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:44.380 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:44.380 INFO  Funcotator - Deflater: IntelDeflater
15:41:44.380 INFO  Funcotator - Inflater: IntelInflater
15:41:44.380 INFO  Funcotator - GCS max retries/reopens: 20
15:41:44.380 INFO  Funcotator - Requester pays: disabled
15:41:44.380 INFO  Funcotator - Initializing engine
15:41:44.381 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
15:41:44.400 INFO  Funcotator - Done initializing engine
15:41:44.400 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:44.400 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:44.400 INFO  Funcotator - Initializing data sources...
15:41:44.400 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:44.400 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:44.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
15:41:44.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
15:41:44.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:44.400 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:44.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
15:41:44.400 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:44.401 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
15:41:44.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
15:41:44.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:44.402 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:44.402 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:44.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:44.418 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:41:44.426 INFO  Funcotator - Initializing Funcotator Engine...
15:41:44.434 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:44.434 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16211218606101813310.vcf
15:41:44.488 INFO  ProgressMeter - Starting traversal
15:41:44.488 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:44.514 INFO  ProgressMeter -             unmapped              0.0                   100         230769.2
15:41:44.514 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:41:44.514 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:41:44.519 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:44.520 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16211218606101813310.vcf
15:41:44.634 INFO  Funcotator - ------------------------------------------------------------
15:41:44.634 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:44.634 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:44.634 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:44.634 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:44.634 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:44 PM UTC
15:41:44.634 INFO  Funcotator - ------------------------------------------------------------
15:41:44.634 INFO  Funcotator - ------------------------------------------------------------
15:41:44.634 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:44.634 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:44.634 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:44.634 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:44.634 INFO  Funcotator - Deflater: IntelDeflater
15:41:44.634 INFO  Funcotator - Inflater: IntelInflater
15:41:44.634 INFO  Funcotator - GCS max retries/reopens: 20
15:41:44.634 INFO  Funcotator - Requester pays: disabled
15:41:44.634 INFO  Funcotator - Initializing engine
15:41:44.637 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
15:41:44.638 INFO  Funcotator - Done initializing engine
15:41:44.638 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:44.638 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:44.638 INFO  Funcotator - Initializing data sources...
15:41:44.638 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/
15:41:44.638 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:44.638 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
15:41:44.638 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
15:41:44.638 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
15:41:44.638 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:44.638 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
15:41:44.638 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:44.639 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
15:41:44.639 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
15:41:44.640 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
15:41:44.640 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:41:44.640 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
15:41:44.643 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
15:41:44.645 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
15:41:44.648 INFO  Funcotator - Initializing Funcotator Engine...
15:41:44.648 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:44.648 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.
15:41:44.648 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:44.648 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing10957316598708452355.vcf
15:41:44.651 INFO  ProgressMeter - Starting traversal
15:41:44.651 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:44.673 INFO  ProgressMeter -             unmapped              0.0                     1           2727.3
15:41:44.673 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:41:44.673 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
15:41:44.675 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:44.676 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing10957316598708452355.vcf
15:41:44.747 INFO  Funcotator - ------------------------------------------------------------
15:41:44.747 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:44.747 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:44.747 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:44.747 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:44.747 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:44 PM UTC
15:41:44.747 INFO  Funcotator - ------------------------------------------------------------
15:41:44.747 INFO  Funcotator - ------------------------------------------------------------
15:41:44.747 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:44.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:44.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:44.747 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:44.747 INFO  Funcotator - Deflater: IntelDeflater
15:41:44.747 INFO  Funcotator - Inflater: IntelInflater
15:41:44.747 INFO  Funcotator - GCS max retries/reopens: 20
15:41:44.747 INFO  Funcotator - Requester pays: disabled
15:41:44.747 INFO  Funcotator - Initializing engine
15:41:44.748 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
15:41:44.749 INFO  Funcotator - Done initializing engine
15:41:44.749 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:44.749 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:44.749 INFO  Funcotator - Initializing data sources...
15:41:44.749 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:44.749 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:44.749 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
15:41:44.749 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
15:41:44.750 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
15:41:44.750 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
15:41:44.750 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
15:41:44.750 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
15:41:44.750 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
15:41:44.750 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
15:41:44.751 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
15:41:44.751 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
15:41:44.751 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
15:41:44.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:44.751 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
15:41:44.751 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
15:41:44.752 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
15:41:44.752 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:44.752 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
15:41:44.752 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
15:41:44.795 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
15:41:44.815 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
15:41:44.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:44.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:44.823 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
15:41:44.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:41:45.410 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
15:41:45.449 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
15:41:45.449 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:45.450 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
15:41:45.450 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
15:41:45.532 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:45.532 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:45.533 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
15:41:45.561 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:45.561 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:45.562 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
15:41:45.562 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
15:41:45.563 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
15:41:45.563 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:45.563 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
15:41:45.565 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
15:41:45.568 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
15:41:45.570 INFO  Funcotator - Initializing Funcotator Engine...
15:41:45.570 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
15:41:45.570 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:45.570 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:45.570 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:45.570 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:45.571 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:45.571 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:45.571 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14137465310789298559.vcf
15:41:45.571 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
15:41:45.572 INFO  ProgressMeter - Starting traversal
15:41:45.572 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:45.592 INFO  ProgressMeter -             unmapped              0.0                     3           9000.0
15:41:45.592 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:45.592 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:45.594 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3376414720
15:41:45.660 INFO  Funcotator - ------------------------------------------------------------
15:41:45.660 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:45.660 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:45.660 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:45.660 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:45.660 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:45 PM UTC
15:41:45.660 INFO  Funcotator - ------------------------------------------------------------
15:41:45.660 INFO  Funcotator - ------------------------------------------------------------
15:41:45.660 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:45.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:45.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:45.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:45.660 INFO  Funcotator - Deflater: IntelDeflater
15:41:45.660 INFO  Funcotator - Inflater: IntelInflater
15:41:45.660 INFO  Funcotator - GCS max retries/reopens: 20
15:41:45.660 INFO  Funcotator - Requester pays: disabled
15:41:45.660 INFO  Funcotator - Initializing engine
15:41:45.661 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
15:41:45.662 INFO  Funcotator - Done initializing engine
15:41:45.662 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:45.662 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:45.662 INFO  Funcotator - Initializing data sources...
15:41:45.662 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:45.662 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:45.662 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
15:41:45.662 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
15:41:45.663 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:41:45.663 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
15:41:45.663 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
15:41:45.663 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
15:41:45.663 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
15:41:45.663 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
15:41:45.663 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
15:41:45.664 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
15:41:45.664 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
15:41:45.664 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
15:41:45.664 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
15:41:45.664 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
15:41:45.665 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
15:41:45.665 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:45.665 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
15:41:45.665 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
15:41:45.708 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
15:41:45.727 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
15:41:45.735 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
15:41:45.736 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
15:41:45.736 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
15:41:45.736 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
15:41:46.321 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
15:41:46.359 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
15:41:46.359 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:46.360 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
15:41:46.360 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
15:41:46.442 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:46.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:46.443 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
15:41:46.470 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:46.470 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:46.470 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
15:41:46.471 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
15:41:46.471 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
15:41:46.471 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:46.472 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
15:41:46.474 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
15:41:46.477 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
15:41:46.479 INFO  Funcotator - Initializing Funcotator Engine...
15:41:46.479 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:46.479 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:46.479 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11508739575517549644.vcf
15:41:46.480 INFO  ProgressMeter - Starting traversal
15:41:46.480 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:46.656 INFO  ProgressMeter -             unmapped              0.0                     4           1363.6
15:41:46.656 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:46.656 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:46.657 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:46 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3376414720
15:41:46.724 INFO  Funcotator - ------------------------------------------------------------
15:41:46.724 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:46.724 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:46.724 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:46.724 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:46.724 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:46 PM UTC
15:41:46.724 INFO  Funcotator - ------------------------------------------------------------
15:41:46.724 INFO  Funcotator - ------------------------------------------------------------
15:41:46.724 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:46.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:46.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:46.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:46.724 INFO  Funcotator - Deflater: IntelDeflater
15:41:46.724 INFO  Funcotator - Inflater: IntelInflater
15:41:46.724 INFO  Funcotator - GCS max retries/reopens: 20
15:41:46.724 INFO  Funcotator - Requester pays: disabled
15:41:46.724 INFO  Funcotator - Initializing engine
15:41:46.725 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
15:41:46.726 INFO  Funcotator - Done initializing engine
15:41:46.726 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:46.726 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:46.726 INFO  Funcotator - Initializing data sources...
15:41:46.726 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:46.726 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:46.726 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
15:41:46.727 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
15:41:46.727 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
15:41:46.727 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
15:41:46.727 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
15:41:46.727 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
15:41:46.727 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
15:41:46.728 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
15:41:46.728 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
15:41:46.728 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
15:41:46.728 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
15:41:46.728 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
15:41:46.728 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
15:41:46.728 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
15:41:46.729 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
15:41:46.729 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:46.729 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
15:41:46.729 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
15:41:46.776 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
15:41:46.796 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
15:41:46.803 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
15:41:46.803 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
15:41:46.804 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
15:41:46.804 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
15:41:47.427 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
15:41:47.466 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
15:41:47.466 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:47.467 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
15:41:47.467 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
15:41:47.549 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:47.549 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:47.549 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
15:41:47.577 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:47.577 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:47.577 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
15:41:47.577 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
15:41:47.578 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
15:41:47.578 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:47.578 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
15:41:47.580 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
15:41:47.583 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
15:41:47.585 INFO  Funcotator - Initializing Funcotator Engine...
15:41:47.585 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
15:41:47.586 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:47.586 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:47.586 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:47.586 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:47.586 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:47.586 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14386436761775154281.vcf
15:41:47.586 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
15:41:47.588 INFO  ProgressMeter - Starting traversal
15:41:47.588 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:47.608 INFO  ProgressMeter -             unmapped              0.0                     3           9000.0
15:41:47.608 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:47.608 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:47.610 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3376414720
15:41:47.674 INFO  Funcotator - ------------------------------------------------------------
15:41:47.674 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:47.674 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:47.674 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:47.674 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:47.674 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:47 PM UTC
15:41:47.674 INFO  Funcotator - ------------------------------------------------------------
15:41:47.674 INFO  Funcotator - ------------------------------------------------------------
15:41:47.674 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:47.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:47.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:47.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:47.674 INFO  Funcotator - Deflater: IntelDeflater
15:41:47.674 INFO  Funcotator - Inflater: IntelInflater
15:41:47.674 INFO  Funcotator - GCS max retries/reopens: 20
15:41:47.674 INFO  Funcotator - Requester pays: disabled
15:41:47.674 INFO  Funcotator - Initializing engine
15:41:47.674 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
15:41:47.675 INFO  Funcotator - Done initializing engine
15:41:47.675 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:47.675 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:47.675 INFO  Funcotator - Initializing data sources...
15:41:47.675 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:47.675 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:47.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:41:47.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:41:47.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:41:47.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:47.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:47.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:47.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:41:47.676 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
15:41:47.676 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
15:41:47.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:41:47.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:41:47.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:47.677 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
15:41:47.677 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
15:41:47.677 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
15:41:47.677 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:47.677 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
15:41:47.678 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
15:41:47.720 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
15:41:47.738 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
15:41:47.746 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
15:41:47.747 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
15:41:47.747 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
15:41:47.747 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
15:41:48.330 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
15:41:48.369 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
15:41:48.369 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:48.370 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
15:41:48.370 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
15:41:48.452 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:48.452 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:48.452 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
15:41:48.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:48.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:48.480 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
15:41:48.480 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
15:41:48.481 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
15:41:48.481 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:48.481 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:48.484 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
15:41:48.486 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
15:41:48.488 INFO  Funcotator - Initializing Funcotator Engine...
15:41:48.488 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:48.488 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:48.488 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out583187017244092944.vcf
15:41:48.489 INFO  ProgressMeter - Starting traversal
15:41:48.489 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:48.593 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
15:41:48.593 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:48.593 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:48.594 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:48 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3376414720
15:41:48.662 INFO  Funcotator - ------------------------------------------------------------
15:41:48.662 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:48.662 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:48.662 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:48.662 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:48.662 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:48 PM UTC
15:41:48.662 INFO  Funcotator - ------------------------------------------------------------
15:41:48.662 INFO  Funcotator - ------------------------------------------------------------
15:41:48.662 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:48.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:48.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:48.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:48.662 INFO  Funcotator - Deflater: IntelDeflater
15:41:48.662 INFO  Funcotator - Inflater: IntelInflater
15:41:48.662 INFO  Funcotator - GCS max retries/reopens: 20
15:41:48.662 INFO  Funcotator - Requester pays: disabled
15:41:48.662 INFO  Funcotator - Initializing engine
15:41:48.663 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
15:41:48.663 INFO  Funcotator - Done initializing engine
15:41:48.663 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:48.663 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:48.663 INFO  Funcotator - Initializing data sources...
15:41:48.663 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:48.663 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:48.664 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
15:41:48.664 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
15:41:48.664 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
15:41:48.664 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
15:41:48.664 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
15:41:48.664 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
15:41:48.665 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
15:41:48.665 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
15:41:48.665 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
15:41:48.665 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
15:41:48.665 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
15:41:48.665 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:48.665 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
15:41:48.665 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
15:41:48.666 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
15:41:48.666 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:48.666 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
15:41:48.666 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
15:41:48.709 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
15:41:48.728 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
15:41:48.736 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
15:41:48.736 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
15:41:48.736 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
15:41:48.736 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
15:41:49.288 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
15:41:49.372 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
15:41:49.373 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:49.373 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
15:41:49.374 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
15:41:49.455 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:49.455 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:49.456 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
15:41:49.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:49.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:49.483 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
15:41:49.484 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
15:41:49.485 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
15:41:49.485 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:49.486 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
15:41:49.489 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
15:41:49.493 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
15:41:49.496 INFO  Funcotator - Initializing Funcotator Engine...
15:41:49.496 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
15:41:49.496 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:49.496 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:49.496 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:49.496 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:49.496 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:49.496 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:49.496 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:49.497 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:49.497 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:49.497 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out487069857828819734.maf
15:41:49.497 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
15:41:49.498 INFO  ProgressMeter - Starting traversal
15:41:49.498 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:49.528 INFO  ProgressMeter -             unmapped              0.0                     3           6000.0
15:41:49.528 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:49.528 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:49.528 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3376414720
15:41:49.596 INFO  Funcotator - ------------------------------------------------------------
15:41:49.596 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:49.596 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:49.596 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:49.596 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:49.596 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:49 PM UTC
15:41:49.596 INFO  Funcotator - ------------------------------------------------------------
15:41:49.596 INFO  Funcotator - ------------------------------------------------------------
15:41:49.596 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:49.596 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:49.596 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:49.596 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:49.596 INFO  Funcotator - Deflater: IntelDeflater
15:41:49.596 INFO  Funcotator - Inflater: IntelInflater
15:41:49.597 INFO  Funcotator - GCS max retries/reopens: 20
15:41:49.597 INFO  Funcotator - Requester pays: disabled
15:41:49.597 INFO  Funcotator - Initializing engine
15:41:49.597 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
15:41:49.598 INFO  Funcotator - Done initializing engine
15:41:49.598 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:49.598 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:49.598 INFO  Funcotator - Initializing data sources...
15:41:49.598 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:49.598 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:49.598 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
15:41:49.598 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
15:41:49.599 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
15:41:49.599 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
15:41:49.599 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
15:41:49.599 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
15:41:49.599 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
15:41:49.599 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
15:41:49.600 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
15:41:49.600 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
15:41:49.600 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
15:41:49.600 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:49.600 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
15:41:49.600 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
15:41:49.600 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
15:41:49.600 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:49.601 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
15:41:49.601 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
15:41:49.645 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
15:41:49.664 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
15:41:49.672 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
15:41:49.672 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
15:41:49.672 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
15:41:49.672 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
15:41:50.257 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
15:41:50.295 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
15:41:50.295 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:50.296 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
15:41:50.296 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
15:41:50.379 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:50.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:50.379 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:41:50.406 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:50.406 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:50.407 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
15:41:50.407 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
15:41:50.408 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
15:41:50.408 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:50.408 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
15:41:50.410 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
15:41:50.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:50.415 INFO  Funcotator - Initializing Funcotator Engine...
15:41:50.415 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:50.415 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:50.415 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10820988597938782423.maf
15:41:50.415 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
15:41:50.416 INFO  ProgressMeter - Starting traversal
15:41:50.416 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:50.520 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
15:41:50.520 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:50.520 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:50.520 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3376414720
15:41:50.587 INFO  Funcotator - ------------------------------------------------------------
15:41:50.587 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:50.587 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:50.587 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:50.587 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:50.587 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:50 PM UTC
15:41:50.587 INFO  Funcotator - ------------------------------------------------------------
15:41:50.587 INFO  Funcotator - ------------------------------------------------------------
15:41:50.587 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:50.587 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:50.587 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:50.587 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:50.587 INFO  Funcotator - Deflater: IntelDeflater
15:41:50.587 INFO  Funcotator - Inflater: IntelInflater
15:41:50.587 INFO  Funcotator - GCS max retries/reopens: 20
15:41:50.587 INFO  Funcotator - Requester pays: disabled
15:41:50.587 INFO  Funcotator - Initializing engine
15:41:50.588 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
15:41:50.588 INFO  Funcotator - Done initializing engine
15:41:50.588 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:50.588 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:50.588 INFO  Funcotator - Initializing data sources...
15:41:50.588 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:50.588 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:50.589 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
15:41:50.589 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
15:41:50.589 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
15:41:50.589 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
15:41:50.589 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
15:41:50.589 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
15:41:50.589 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
15:41:50.590 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
15:41:50.590 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
15:41:50.590 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
15:41:50.590 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
15:41:50.590 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:50.590 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
15:41:50.590 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
15:41:50.591 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
15:41:50.591 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:50.591 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
15:41:50.591 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
15:41:50.634 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
15:41:50.653 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
15:41:50.660 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
15:41:50.661 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
15:41:50.661 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
15:41:50.661 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
15:41:51.243 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
15:41:51.281 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
15:41:51.281 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:51.282 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
15:41:51.282 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
15:41:51.364 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:51.364 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:51.365 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
15:41:51.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:51.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:51.392 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
15:41:51.393 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
15:41:51.393 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
15:41:51.393 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:51.394 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
15:41:51.396 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
15:41:51.398 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
15:41:51.401 INFO  Funcotator - Initializing Funcotator Engine...
15:41:51.401 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
15:41:51.401 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:41:51.401 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:41:51.401 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:41:51.401 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:41:51.401 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:51.402 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11822967889177634536.maf
15:41:51.402 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
15:41:51.402 INFO  ProgressMeter - Starting traversal
15:41:51.402 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:51.421 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
15:41:51.421 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:41:51.421 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:41:51.421 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3376414720
15:41:51.487 INFO  Funcotator - ------------------------------------------------------------
15:41:51.487 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:51.487 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:51.487 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:51.487 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:51.487 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:51 PM UTC
15:41:51.487 INFO  Funcotator - ------------------------------------------------------------
15:41:51.487 INFO  Funcotator - ------------------------------------------------------------
15:41:51.487 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:51.487 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:51.487 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:51.487 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:51.487 INFO  Funcotator - Deflater: IntelDeflater
15:41:51.487 INFO  Funcotator - Inflater: IntelInflater
15:41:51.487 INFO  Funcotator - GCS max retries/reopens: 20
15:41:51.487 INFO  Funcotator - Requester pays: disabled
15:41:51.487 INFO  Funcotator - Initializing engine
15:41:51.488 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
15:41:51.488 INFO  Funcotator - Done initializing engine
15:41:51.488 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:51.488 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:51.488 INFO  Funcotator - Initializing data sources...
15:41:51.488 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:51.488 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.489 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
15:41:51.490 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
15:41:51.490 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
15:41:51.490 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
15:41:51.490 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:51.490 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
15:41:51.490 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
15:41:51.490 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
15:41:51.490 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:51.490 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
15:41:51.491 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
15:41:51.533 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
15:41:51.552 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
15:41:51.560 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
15:41:51.560 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
15:41:51.560 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
15:41:51.560 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
15:41:52.140 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
15:41:52.179 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
15:41:52.179 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:52.179 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
15:41:52.180 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
15:41:52.314 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:52.314 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:52.315 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
15:41:52.342 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
15:41:52.342 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
WARNING	2025-05-27 15:41:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:52.342 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
15:41:52.343 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
15:41:52.343 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
15:41:52.343 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:52.344 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
15:41:52.346 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
15:41:52.348 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
15:41:52.351 INFO  Funcotator - Initializing Funcotator Engine...
15:41:52.351 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:41:52.351 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:52.351 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17316224252199957724.maf
15:41:52.351 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
15:41:52.351 INFO  ProgressMeter - Starting traversal
15:41:52.351 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:52.454 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
15:41:52.454 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:41:52.454 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:41:52.454 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3376414720
15:41:52.519 INFO  Funcotator - ------------------------------------------------------------
15:41:52.519 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:52.519 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:52.519 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:52.519 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:52.519 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:52 PM UTC
15:41:52.519 INFO  Funcotator - ------------------------------------------------------------
15:41:52.519 INFO  Funcotator - ------------------------------------------------------------
15:41:52.519 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:52.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:52.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:52.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:52.519 INFO  Funcotator - Deflater: IntelDeflater
15:41:52.519 INFO  Funcotator - Inflater: IntelInflater
15:41:52.519 INFO  Funcotator - GCS max retries/reopens: 20
15:41:52.519 INFO  Funcotator - Requester pays: disabled
15:41:52.519 INFO  Funcotator - Initializing engine
15:41:52.520 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
15:41:52.545 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:41:52.545 INFO  Funcotator - Done initializing engine
15:41:52.545 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:52.545 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:52.545 INFO  Funcotator - Initializing data sources...
15:41:52.545 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/
15:41:52.545 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:52.545 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
15:41:52.545 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
15:41:52.545 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
15:41:52.545 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:52.545 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
15:41:52.545 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:52.546 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
15:41:52.547 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
15:41:52.547 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
15:41:52.547 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:52.548 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
15:41:52.561 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
15:41:52.573 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
15:41:52.581 INFO  Funcotator - Initializing Funcotator Engine...
15:41:52.585 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:52.586 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5447865297919436966.vcf
15:41:52.598 INFO  ProgressMeter - Starting traversal
15:41:52.598 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:52.610 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
15:41:52.610 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:41:52.610 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:41:52.615 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:52.680 INFO  Funcotator - ------------------------------------------------------------
15:41:52.680 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:52.680 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:52.680 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:52.680 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:52.680 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:52 PM UTC
15:41:52.680 INFO  Funcotator - ------------------------------------------------------------
15:41:52.680 INFO  Funcotator - ------------------------------------------------------------
15:41:52.680 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:52.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:52.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:52.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:52.680 INFO  Funcotator - Deflater: IntelDeflater
15:41:52.680 INFO  Funcotator - Inflater: IntelInflater
15:41:52.680 INFO  Funcotator - GCS max retries/reopens: 20
15:41:52.680 INFO  Funcotator - Requester pays: disabled
15:41:52.680 INFO  Funcotator - Initializing engine
15:41:52.681 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
15:41:52.700 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:41:52.700 INFO  Funcotator - Done initializing engine
15:41:52.700 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:52.700 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:52.700 INFO  Funcotator - Initializing data sources...
15:41:52.700 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/
15:41:52.700 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:52.701 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
15:41:52.701 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
15:41:52.701 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
15:41:52.701 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:52.701 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
15:41:52.701 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:52.702 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
15:41:52.702 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
15:41:52.703 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
15:41:52.703 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:52.703 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
15:41:52.711 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
15:41:52.719 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
15:41:52.726 INFO  Funcotator - Initializing Funcotator Engine...
15:41:52.730 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:52.730 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13662422553946758553.vcf
15:41:52.742 INFO  ProgressMeter - Starting traversal
15:41:52.742 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:52.754 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
15:41:52.754 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:41:52.754 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:41:52.759 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:52.759 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out5447865297919436966.vcf
15:41:52.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13662422553946758553.vcf
15:41:52.847 INFO  Funcotator - ------------------------------------------------------------
15:41:52.847 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:52.847 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:52.847 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:52.847 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:52.847 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:52 PM UTC
15:41:52.847 INFO  Funcotator - ------------------------------------------------------------
15:41:52.847 INFO  Funcotator - ------------------------------------------------------------
15:41:52.847 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:52.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:52.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:52.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:52.847 INFO  Funcotator - Deflater: IntelDeflater
15:41:52.847 INFO  Funcotator - Inflater: IntelInflater
15:41:52.847 INFO  Funcotator - GCS max retries/reopens: 20
15:41:52.847 INFO  Funcotator - Requester pays: disabled
15:41:52.847 INFO  Funcotator - Initializing engine
15:41:52.848 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
15:41:52.849 INFO  Funcotator - Done initializing engine
15:41:52.849 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:52.849 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:52.849 INFO  Funcotator - Initializing data sources...
15:41:52.849 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:52.849 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:52.849 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
15:41:52.849 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
15:41:52.849 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
15:41:52.849 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:52.849 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
15:41:52.850 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:52.850 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
15:41:52.850 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
15:41:52.851 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:41:52.851 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:52.851 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
15:41:52.852 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:41:52.853 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:41:52.854 INFO  Funcotator - Initializing Funcotator Engine...
15:41:52.854 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:52.854 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.
15:41:52.854 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4000348372761708912.maf
15:41:52.854 INFO  ProgressMeter - Starting traversal
15:41:52.854 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:52.856 WARN  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
15:41:52.857 WARN  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
15:41:52.857 WARN  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
15:41:52.859 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:41:52.860 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:41:52.861 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:41:52.862 INFO  ProgressMeter -             unmapped              0.0                     6          45000.0
15:41:52.862 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:41:52.862 WARN  Funcotator - ================================================================================
15:41:52.862 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:41:52.862 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:41:52.862 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:41:52.862 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:41:52.862 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:41:52.862 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:41:52.862 WARN  Funcotator - --------------------------------------------------------------------------------
15:41:52.862 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:41:52.862 WARN  Funcotator -  run was misconfigured.     
15:41:52.862 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:41:52.862 WARN  Funcotator - ================================================================================
15:41:52.862 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:52.862 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:52.935 INFO  Funcotator - ------------------------------------------------------------
15:41:52.935 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:52.935 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:52.935 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:52.935 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:52.935 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:52 PM UTC
15:41:52.935 INFO  Funcotator - ------------------------------------------------------------
15:41:52.935 INFO  Funcotator - ------------------------------------------------------------
15:41:52.935 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:52.935 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:52.935 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:52.935 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:52.935 INFO  Funcotator - Deflater: IntelDeflater
15:41:52.935 INFO  Funcotator - Inflater: IntelInflater
15:41:52.935 INFO  Funcotator - GCS max retries/reopens: 20
15:41:52.935 INFO  Funcotator - Requester pays: disabled
15:41:52.935 INFO  Funcotator - Initializing engine
15:41:52.936 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
15:41:52.937 INFO  Funcotator - Done initializing engine
15:41:52.937 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:52.937 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:52.937 INFO  Funcotator - Initializing data sources...
15:41:52.937 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:52.937 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:52.938 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
15:41:52.938 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
15:41:52.938 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
15:41:52.938 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:52.938 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
15:41:52.938 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:52.938 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
15:41:52.939 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
15:41:52.939 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
15:41:52.939 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:52.940 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
15:41:52.940 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
15:41:52.941 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
15:41:52.942 INFO  Funcotator - Initializing Funcotator Engine...
15:41:52.942 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:52.942 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.
15:41:52.942 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out73404575628254259.maf
15:41:52.943 INFO  ProgressMeter - Starting traversal
15:41:52.943 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:52.944 WARN  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
15:41:52.945 WARN  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
15:41:52.945 WARN  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
15:41:52.946 WARN  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=
15:41:52.946 WARN  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=
15:41:52.948 WARN  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=
15:41:52.948 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
15:41:52.948 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:41:52.948 WARN  Funcotator - ================================================================================
15:41:52.948 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:41:52.948 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:41:52.948 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:41:52.948 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:41:52.948 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:41:52.948 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:41:52.948 WARN  Funcotator - --------------------------------------------------------------------------------
15:41:52.948 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:41:52.948 WARN  Funcotator -  run was misconfigured.     
15:41:52.948 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:41:52.948 WARN  Funcotator - ================================================================================
15:41:52.948 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:52.948 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.018 INFO  Funcotator - ------------------------------------------------------------
15:41:53.018 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.018 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.018 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.018 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.018 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.018 INFO  Funcotator - ------------------------------------------------------------
15:41:53.018 INFO  Funcotator - ------------------------------------------------------------
15:41:53.018 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.018 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.018 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.018 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.018 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.018 INFO  Funcotator - Inflater: IntelInflater
15:41:53.018 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.018 INFO  Funcotator - Requester pays: disabled
15:41:53.018 INFO  Funcotator - Initializing engine
15:41:53.019 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
15:41:53.020 INFO  Funcotator - Done initializing engine
15:41:53.020 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:53.020 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.020 INFO  Funcotator - Initializing data sources...
15:41:53.020 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:53.020 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.020 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
15:41:53.020 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
15:41:53.021 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
15:41:53.021 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.021 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
15:41:53.021 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:53.021 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
15:41:53.021 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
15:41:53.022 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
15:41:53.022 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:53.022 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
15:41:53.023 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
15:41:53.024 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
15:41:53.025 INFO  Funcotator - Initializing Funcotator Engine...
15:41:53.025 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:53.025 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.
15:41:53.025 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5679359699764362145.maf
15:41:53.025 INFO  ProgressMeter - Starting traversal
15:41:53.025 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:53.027 WARN  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
15:41:53.027 WARN  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
15:41:53.027 WARN  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
15:41:53.029 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 @ 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=
15:41:53.029 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 @ 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=
15:41:53.030 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 @ 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=
15:41:53.030 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
15:41:53.030 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:41:53.030 WARN  Funcotator - ================================================================================
15:41:53.030 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:41:53.030 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:41:53.030 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:41:53.030 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:41:53.030 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:41:53.030 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:41:53.030 WARN  Funcotator - --------------------------------------------------------------------------------
15:41:53.030 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:41:53.030 WARN  Funcotator -  run was misconfigured.     
15:41:53.030 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:41:53.030 WARN  Funcotator - ================================================================================
15:41:53.030 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:53.030 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.102 INFO  Funcotator - ------------------------------------------------------------
15:41:53.102 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.102 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.102 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.102 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.102 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.102 INFO  Funcotator - ------------------------------------------------------------
15:41:53.102 INFO  Funcotator - ------------------------------------------------------------
15:41:53.102 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.102 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.102 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.102 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.102 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.102 INFO  Funcotator - Inflater: IntelInflater
15:41:53.102 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.102 INFO  Funcotator - Requester pays: disabled
15:41:53.102 INFO  Funcotator - Initializing engine
15:41:53.103 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
15:41:53.104 INFO  Funcotator - Done initializing engine
15:41:53.104 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:53.104 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.104 INFO  Funcotator - Initializing data sources...
15:41:53.104 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:53.104 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.104 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
15:41:53.104 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
15:41:53.104 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
15:41:53.104 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.104 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
15:41:53.105 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:53.105 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
15:41:53.105 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
15:41:53.106 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
15:41:53.106 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:53.106 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
15:41:53.107 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
15:41:53.108 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
15:41:53.109 INFO  Funcotator - Initializing Funcotator Engine...
15:41:53.109 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:53.109 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.
15:41:53.109 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11268441966087438677.maf
15:41:53.109 INFO  ProgressMeter - Starting traversal
15:41:53.109 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:53.110 WARN  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
15:41:53.111 WARN  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
15:41:53.111 WARN  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
15:41:53.112 WARN  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=
15:41:53.113 WARN  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=
15:41:53.114 WARN  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=
15:41:53.114 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
15:41:53.114 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:41:53.114 WARN  Funcotator - ================================================================================
15:41:53.114 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:41:53.114 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:41:53.114 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:41:53.114 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:41:53.114 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:41:53.114 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:41:53.114 WARN  Funcotator - --------------------------------------------------------------------------------
15:41:53.114 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:41:53.114 WARN  Funcotator -  run was misconfigured.     
15:41:53.114 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:41:53.114 WARN  Funcotator - ================================================================================
15:41:53.114 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:53.114 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.184 INFO  Funcotator - ------------------------------------------------------------
15:41:53.184 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.184 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.184 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.184 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.184 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.184 INFO  Funcotator - ------------------------------------------------------------
15:41:53.184 INFO  Funcotator - ------------------------------------------------------------
15:41:53.184 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.184 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.184 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.184 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.184 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.184 INFO  Funcotator - Inflater: IntelInflater
15:41:53.184 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.184 INFO  Funcotator - Requester pays: disabled
15:41:53.184 INFO  Funcotator - Initializing engine
15:41:53.185 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
15:41:53.186 INFO  Funcotator - Done initializing engine
15:41:53.186 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:53.186 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.186 INFO  Funcotator - Initializing data sources...
15:41:53.186 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:53.186 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.186 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
15:41:53.186 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
15:41:53.187 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
15:41:53.187 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.187 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
15:41:53.187 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:53.187 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
15:41:53.187 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
15:41:53.188 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
15:41:53.188 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:53.188 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
15:41:53.189 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
15:41:53.190 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
15:41:53.191 INFO  Funcotator - Initializing Funcotator Engine...
15:41:53.191 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:53.191 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.
15:41:53.191 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15216638835604584533.vcf
15:41:53.194 INFO  ProgressMeter - Starting traversal
15:41:53.194 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:53.204 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:41:53.204 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:41:53.204 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:41:53.206 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.207 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15216638835604584533.vcf
15:41:53.276 INFO  Funcotator - ------------------------------------------------------------
15:41:53.276 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.277 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.277 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.277 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.277 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.277 INFO  Funcotator - ------------------------------------------------------------
15:41:53.277 INFO  Funcotator - ------------------------------------------------------------
15:41:53.277 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.277 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.277 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.277 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.277 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.277 INFO  Funcotator - Inflater: IntelInflater
15:41:53.277 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.277 INFO  Funcotator - Requester pays: disabled
15:41:53.277 INFO  Funcotator - Initializing engine
15:41:53.278 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
15:41:53.279 INFO  Funcotator - Done initializing engine
15:41:53.279 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:53.279 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.279 INFO  Funcotator - Initializing data sources...
15:41:53.279 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:53.279 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.279 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
15:41:53.279 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
15:41:53.279 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
15:41:53.279 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.279 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
15:41:53.279 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:53.280 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
15:41:53.280 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
15:41:53.280 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
15:41:53.280 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:53.281 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
15:41:53.281 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
15:41:53.283 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
15:41:53.283 INFO  Funcotator - Initializing Funcotator Engine...
15:41:53.283 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:41:53.283 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.
15:41:53.283 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out18146487329351094939.maf
15:41:53.284 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:53.284 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.351 INFO  Funcotator - ------------------------------------------------------------
15:41:53.351 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.351 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.351 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.351 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.352 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.352 INFO  Funcotator - ------------------------------------------------------------
15:41:53.352 INFO  Funcotator - ------------------------------------------------------------
15:41:53.352 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.352 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.352 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.352 INFO  Funcotator - Inflater: IntelInflater
15:41:53.352 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.352 INFO  Funcotator - Requester pays: disabled
15:41:53.352 INFO  Funcotator - Initializing engine
15:41:53.352 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
15:41:53.365 INFO  Funcotator - Done initializing engine
15:41:53.365 INFO  Funcotator - Skipping sequence dictionary validation.
15:41:53.365 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.365 INFO  Funcotator - Initializing data sources...
15:41:53.365 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:41:53.365 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.365 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
15:41:53.365 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
15:41:53.365 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
15:41:53.365 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.365 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
15:41:53.365 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:53.366 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
15:41:53.366 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
15:41:53.367 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
15:41:53.367 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:41:53.367 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
15:41:53.375 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
15:41:53.383 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
15:41:53.391 INFO  Funcotator - Initializing Funcotator Engine...
15:41:53.395 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:41:53.395 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9781923658840742780.maf
15:41:53.395 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
15:41:53.396 INFO  ProgressMeter - Starting traversal
15:41:53.396 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:53.398 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)
15:41:53.398 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)
15:41:53.398 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.398 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:53.398 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:41:53.398 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:41:53.399 WARN  MafOutputRenderer - 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+
15:41:53.403 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.403 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:53.403 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:41:53.403 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:41:53.404 WARN  MafOutputRenderer - 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+
15:41:53.404 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)
15:41:53.404 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)
15:41:53.404 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.404 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:53.405 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:41:53.405 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:41:53.405 WARN  MafOutputRenderer - 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+
15:41:53.405 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)
15:41:53.405 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)
15:41:53.405 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:41:53.405 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:41:53.406 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:41:53.406 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:41:53.406 WARN  MafOutputRenderer - 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+
15:41:53.406 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.406 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:53.407 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:41:53.407 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:41:53.407 WARN  MafOutputRenderer - 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+
15:41:53.407 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.407 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:53.408 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:41:53.408 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:41:53.408 WARN  MafOutputRenderer - 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=
15:41:53.408 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)
15:41:53.409 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)
15:41:53.409 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:41:53.409 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:53.409 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:41:53.409 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:41:53.409 WARN  MafOutputRenderer - 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=
15:41:53.409 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)
15:41:53.410 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)
15:41:53.410 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.410 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:53.410 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:41:53.410 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:41:53.410 WARN  MafOutputRenderer - 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+
15:41:53.411 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:41:53.411 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:41:53.411 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:41:53.411 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:41:53.411 WARN  MafOutputRenderer - 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+
15:41:53.412 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)
15:41:53.412 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)
15:41:53.412 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:41:53.412 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:41:53.412 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:41:53.412 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:41:53.412 WARN  MafOutputRenderer - 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=
15:41:53.413 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
15:41:53.413 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:41:53.413 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:41:53.413 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.557 INFO  Funcotator - ------------------------------------------------------------
15:41:53.557 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.557 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.557 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.557 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.557 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.557 INFO  Funcotator - ------------------------------------------------------------
15:41:53.557 INFO  Funcotator - ------------------------------------------------------------
15:41:53.557 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.557 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.557 INFO  Funcotator - Inflater: IntelInflater
15:41:53.557 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.557 INFO  Funcotator - Requester pays: disabled
15:41:53.558 INFO  Funcotator - Initializing engine
15:41:53.559 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
15:41:53.560 INFO  Funcotator - Done initializing engine
15:41:53.560 INFO  Funcotator - Validating sequence dictionaries...
15:41:53.560 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:41:53.625 INFO  Funcotator - ------------------------------------------------------------
15:41:53.625 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:53.625 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:53.625 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:53.625 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:53.625 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:53 PM UTC
15:41:53.625 INFO  Funcotator - ------------------------------------------------------------
15:41:53.625 INFO  Funcotator - ------------------------------------------------------------
15:41:53.625 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:53.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:53.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:53.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:53.625 INFO  Funcotator - Deflater: IntelDeflater
15:41:53.625 INFO  Funcotator - Inflater: IntelInflater
15:41:53.625 INFO  Funcotator - GCS max retries/reopens: 20
15:41:53.625 INFO  Funcotator - Requester pays: disabled
15:41:53.625 INFO  Funcotator - Initializing engine
15:41:53.627 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
15:41:53.628 INFO  Funcotator - Done initializing engine
15:41:53.628 INFO  Funcotator - Validating sequence dictionaries...
15:41:53.628 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:53.628 INFO  Funcotator - Initializing data sources...
15:41:53.628 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:53.628 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:53.629 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
15:41:53.629 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
15:41:53.629 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
15:41:53.629 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
15:41:53.629 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
15:41:53.629 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
15:41:53.630 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
15:41:53.630 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
15:41:53.630 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
15:41:53.630 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
15:41:53.630 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
15:41:53.630 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:53.630 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
15:41:53.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:41:53.631 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
15:41:53.631 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:53.631 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
15:41:53.631 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
15:41:53.674 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
15:41:53.692 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
15:41:53.699 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
15:41:53.699 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
15:41:53.699 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
15:41:53.700 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
15:41:54.319 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
15:41:54.358 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
15:41:54.358 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:54.359 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
15:41:54.359 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
15:41:54.500 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:54.500 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:54.500 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
15:41:54.528 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
15:41:54.528 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
WARNING	2025-05-27 15:41:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:54.528 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
15:41:54.529 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
15:41:54.529 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
15:41:54.529 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:54.530 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
15:41:54.532 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
15:41:54.535 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
15:41:54.537 INFO  Funcotator - Initializing Funcotator Engine...
15:41:54.537 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:54.537 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.
15:41:54.537 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11668464614959214425.vcf
15:41:54.539 INFO  ProgressMeter - Starting traversal
15:41:54.539 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:56.570 INFO  ProgressMeter -             unmapped              0.0                   198           5849.3
15:41:56.570 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:56.570 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:56.578 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3376414720
15:41:56.648 INFO  Funcotator - ------------------------------------------------------------
15:41:56.648 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:56.648 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:56.648 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:56.648 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:56.648 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:56 PM UTC
15:41:56.648 INFO  Funcotator - ------------------------------------------------------------
15:41:56.648 INFO  Funcotator - ------------------------------------------------------------
15:41:56.648 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:56.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:56.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:56.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:56.648 INFO  Funcotator - Deflater: IntelDeflater
15:41:56.648 INFO  Funcotator - Inflater: IntelInflater
15:41:56.648 INFO  Funcotator - GCS max retries/reopens: 20
15:41:56.648 INFO  Funcotator - Requester pays: disabled
15:41:56.648 INFO  Funcotator - Initializing engine
15:41:56.650 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
15:41:56.651 INFO  Funcotator - Done initializing engine
15:41:56.651 INFO  Funcotator - Validating sequence dictionaries...
15:41:56.651 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:56.651 INFO  Funcotator - Initializing data sources...
15:41:56.651 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:56.651 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:56.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:41:56.652 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
15:41:56.652 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
15:41:56.652 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
15:41:56.652 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
15:41:56.653 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
15:41:56.653 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
15:41:56.653 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
15:41:56.653 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
15:41:56.653 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
15:41:56.653 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
15:41:56.653 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:56.654 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
15:41:56.654 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
15:41:56.654 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
15:41:56.654 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:56.654 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
15:41:56.654 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
15:41:56.697 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
15:41:56.715 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:41:56.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:41:56.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:41:56.722 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:41:56.723 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:41:57.315 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
15:41:57.394 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
15:41:57.394 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:41:57.395 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
15:41:57.396 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
15:41:57.480 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:41:57.481 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:57.481 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
15:41:57.508 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:41:57.509 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:41:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:41:57.509 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
15:41:57.509 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
15:41:57.510 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
15:41:57.510 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:41:57.511 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:41:57.513 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
15:41:57.515 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
15:41:57.517 INFO  Funcotator - Initializing Funcotator Engine...
15:41:57.517 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:41:57.517 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.
15:41:57.518 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator13701252006615925080.maf
15:41:57.518 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
15:41:57.518 INFO  ProgressMeter - Starting traversal
15:41:57.518 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:41:59.486 INFO  ProgressMeter -             unmapped              0.0                   198           6036.6
15:41:59.486 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:41:59.487 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:41:59.487 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:41:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3376414720
15:41:59.554 INFO  Funcotator - ------------------------------------------------------------
15:41:59.554 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:41:59.554 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:41:59.554 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:41:59.554 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:41:59.554 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:41:59 PM UTC
15:41:59.554 INFO  Funcotator - ------------------------------------------------------------
15:41:59.554 INFO  Funcotator - ------------------------------------------------------------
15:41:59.554 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:41:59.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:41:59.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:41:59.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:41:59.554 INFO  Funcotator - Deflater: IntelDeflater
15:41:59.554 INFO  Funcotator - Inflater: IntelInflater
15:41:59.554 INFO  Funcotator - GCS max retries/reopens: 20
15:41:59.554 INFO  Funcotator - Requester pays: disabled
15:41:59.554 INFO  Funcotator - Initializing engine
15:41:59.582 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
15:41:59.603 INFO  Funcotator - Done initializing engine
15:41:59.603 INFO  Funcotator - Validating sequence dictionaries...
15:41:59.610 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:41:59.610 INFO  Funcotator - Initializing data sources...
15:41:59.610 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:41:59.610 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:41:59.610 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
15:41:59.611 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
15:41:59.611 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
15:41:59.611 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
15:41:59.611 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
15:41:59.611 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
15:41:59.611 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
15:41:59.611 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
15:41:59.612 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
15:41:59.612 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
15:41:59.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
15:41:59.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:41:59.612 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
15:41:59.612 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:41:59.612 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
15:41:59.654 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
15:41:59.673 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
15:41:59.681 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
15:41:59.681 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
15:41:59.681 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
15:41:59.682 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
15:42:00.259 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
15:42:00.324 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
15:42:00.325 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.325 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
15:42:00.326 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
15:42:00.327 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
15:42:00.327 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
15:42:00.327 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
15:42:00.328 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:42:00.328 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
15:42:00.329 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
15:42:00.331 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
15:42:00.332 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.336 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:42:00.336 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator12442170034123377387.vcf
15:42:00.337 INFO  ProgressMeter - Starting traversal
15:42:00.337 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.341 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:42:00.345 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3376414720
15:42:00.412 INFO  Funcotator - ------------------------------------------------------------
15:42:00.412 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.412 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.412 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.412 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.412 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.412 INFO  Funcotator - ------------------------------------------------------------
15:42:00.412 INFO  Funcotator - ------------------------------------------------------------
15:42:00.412 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.412 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.412 INFO  Funcotator - Inflater: IntelInflater
15:42:00.412 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.412 INFO  Funcotator - Requester pays: disabled
15:42:00.412 INFO  Funcotator - Initializing engine
15:42:00.416 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
15:42:00.417 INFO  Funcotator - Done initializing engine
15:42:00.417 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.417 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.417 INFO  Funcotator - Initializing data sources...
15:42:00.417 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
15:42:00.417 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.417 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
15:42:00.417 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
15:42:00.417 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
15:42:00.417 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.417 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
15:42:00.417 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.418 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
15:42:00.418 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
15:42:00.419 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
15:42:00.419 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:42:00.419 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
15:42:00.419 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
15:42:00.420 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
15:42:00.420 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.420 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.420 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.
15:42:00.420 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:00.420 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing12448860577554907192.vcf
15:42:00.421 INFO  ProgressMeter - Starting traversal
15:42:00.421 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.425 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
15:42:00.425 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:42:00.425 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
15:42:00.427 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.428 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing12448860577554907192.vcf
15:42:00.497 INFO  Funcotator - ------------------------------------------------------------
15:42:00.497 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.497 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.497 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.497 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.497 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.497 INFO  Funcotator - ------------------------------------------------------------
15:42:00.497 INFO  Funcotator - ------------------------------------------------------------
15:42:00.497 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.497 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.497 INFO  Funcotator - Inflater: IntelInflater
15:42:00.497 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.497 INFO  Funcotator - Requester pays: disabled
15:42:00.497 INFO  Funcotator - Initializing engine
15:42:00.498 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
15:42:00.499 INFO  Funcotator - Done initializing engine
15:42:00.499 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.499 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.499 INFO  Funcotator - Initializing data sources...
15:42:00.499 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.499 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.500 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
15:42:00.500 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
15:42:00.500 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
15:42:00.500 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.500 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
15:42:00.500 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.501 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
15:42:00.501 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
15:42:00.501 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
15:42:00.501 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.502 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
15:42:00.503 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
15:42:00.505 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
15:42:00.506 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.506 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.506 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.
15:42:00.506 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10712115216845640990.maf
15:42:00.506 INFO  ProgressMeter - Starting traversal
15:42:00.507 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.509 WARN  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=
15:42:00.510 WARN  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=
15:42:00.510 WARN  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=
15:42:00.511 WARN  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=
15:42:00.511 WARN  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=
15:42:00.512 WARN  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=
15:42:00.513 WARN  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=
15:42:00.513 WARN  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=
15:42:00.514 WARN  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=
15:42:00.514 WARN  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=
15:42:00.515 WARN  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=
15:42:00.515 WARN  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=
15:42:00.516 WARN  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=
15:42:00.516 WARN  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=
15:42:00.517 WARN  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=
15:42:00.517 WARN  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=
15:42:00.518 WARN  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=
15:42:00.518 WARN  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=
15:42:00.519 WARN  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=
15:42:00.519 WARN  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=
15:42:00.519 WARN  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=
15:42:00.520 INFO  ProgressMeter -             unmapped              0.0                    21          96923.1
15:42:00.520 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:42:00.520 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:42:00.520 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.524 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
15:42:00.526 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
15:42:00.603 INFO  Funcotator - ------------------------------------------------------------
15:42:00.603 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.603 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.603 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.603 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.603 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.603 INFO  Funcotator - ------------------------------------------------------------
15:42:00.603 INFO  Funcotator - ------------------------------------------------------------
15:42:00.603 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.603 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.603 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.603 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.603 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.603 INFO  Funcotator - Inflater: IntelInflater
15:42:00.603 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.603 INFO  Funcotator - Requester pays: disabled
15:42:00.603 INFO  Funcotator - Initializing engine
15:42:00.604 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
15:42:00.605 INFO  Funcotator - Done initializing engine
15:42:00.605 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.605 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.605 INFO  Funcotator - Initializing data sources...
15:42:00.605 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.605 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.606 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
15:42:00.606 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
15:42:00.606 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
15:42:00.606 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.606 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
15:42:00.606 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.607 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
15:42:00.607 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
15:42:00.607 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
15:42:00.607 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.608 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
15:42:00.608 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
15:42:00.609 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
15:42:00.610 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.610 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.610 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.
15:42:00.611 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7722820502876963641.vcf
15:42:00.614 INFO  ProgressMeter - Starting traversal
15:42:00.614 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.622 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
15:42:00.622 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:42:00.622 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:42:00.624 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7722820502876963641.vcf
15:42:00.697 INFO  Funcotator - ------------------------------------------------------------
15:42:00.697 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.697 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.697 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.697 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.697 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.697 INFO  Funcotator - ------------------------------------------------------------
15:42:00.697 INFO  Funcotator - ------------------------------------------------------------
15:42:00.697 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.697 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.697 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.697 INFO  Funcotator - Inflater: IntelInflater
15:42:00.697 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.697 INFO  Funcotator - Requester pays: disabled
15:42:00.697 INFO  Funcotator - Initializing engine
15:42:00.698 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
15:42:00.699 INFO  Funcotator - Done initializing engine
15:42:00.699 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.699 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.699 INFO  Funcotator - Initializing data sources...
15:42:00.699 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.699 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.699 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
15:42:00.699 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
15:42:00.699 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
15:42:00.699 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.699 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
15:42:00.699 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.700 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
15:42:00.700 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
15:42:00.700 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
15:42:00.700 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.701 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
15:42:00.702 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
15:42:00.703 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
15:42:00.704 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.704 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.704 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.
15:42:00.704 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:00.704 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14740622706368455816.vcf
15:42:00.705 INFO  ProgressMeter - Starting traversal
15:42:00.705 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.709 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
15:42:00.709 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:42:00.709 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:42:00.712 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.713 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14740622706368455816.vcf
15:42:00.785 INFO  Funcotator - ------------------------------------------------------------
15:42:00.785 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.785 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.785 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.785 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.785 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.785 INFO  Funcotator - ------------------------------------------------------------
15:42:00.785 INFO  Funcotator - ------------------------------------------------------------
15:42:00.785 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.785 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.785 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.785 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.785 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.785 INFO  Funcotator - Inflater: IntelInflater
15:42:00.785 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.785 INFO  Funcotator - Requester pays: disabled
15:42:00.785 INFO  Funcotator - Initializing engine
15:42:00.786 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
15:42:00.786 INFO  Funcotator - Done initializing engine
15:42:00.786 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.786 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.786 INFO  Funcotator - Initializing data sources...
15:42:00.786 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.786 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.786 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
15:42:00.786 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
15:42:00.786 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
15:42:00.786 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.787 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
15:42:00.787 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.787 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
15:42:00.787 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
15:42:00.788 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
15:42:00.788 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.788 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
15:42:00.789 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
15:42:00.790 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
15:42:00.791 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.791 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.791 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.
15:42:00.791 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:00.791 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8967209735582558315.vcf
15:42:00.791 INFO  ProgressMeter - Starting traversal
15:42:00.791 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.799 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
15:42:00.799 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:42:00.799 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:42:00.801 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.871 INFO  Funcotator - ------------------------------------------------------------
15:42:00.871 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.871 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.871 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.871 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.871 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.871 INFO  Funcotator - ------------------------------------------------------------
15:42:00.871 INFO  Funcotator - ------------------------------------------------------------
15:42:00.871 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.871 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.871 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.871 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.871 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.871 INFO  Funcotator - Inflater: IntelInflater
15:42:00.871 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.871 INFO  Funcotator - Requester pays: disabled
15:42:00.871 INFO  Funcotator - Initializing engine
15:42:00.872 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
15:42:00.872 INFO  Funcotator - Done initializing engine
15:42:00.872 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.872 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.872 INFO  Funcotator - Initializing data sources...
15:42:00.872 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.872 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.873 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
15:42:00.873 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
15:42:00.873 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:42:00.873 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.873 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
15:42:00.873 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.874 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
15:42:00.874 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
15:42:00.874 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
15:42:00.874 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.875 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:42:00.876 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
15:42:00.878 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
15:42:00.879 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.879 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.879 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.
15:42:00.879 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:00.879 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5661896692302887460.maf
15:42:00.879 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
15:42:00.879 INFO  ProgressMeter - Starting traversal
15:42:00.879 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:00.882 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
15:42:00.883 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.884 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.884 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
15:42:00.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
15:42:00.885 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:42:00.886 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:42:00.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.887 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:42:00.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178943785 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:42:00.888 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178947158 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:42:00.889 WARN  MafOutputRenderer - 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=
15:42:00.889 INFO  ProgressMeter -             unmapped              0.0                    15          90000.0
15:42:00.889 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:42:00.889 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:42:00.889 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:00.890 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8967209735582558315.vcf
15:42:00.964 INFO  Funcotator - ------------------------------------------------------------
15:42:00.964 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:00.964 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:00.964 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:00.964 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:00.964 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:00 PM UTC
15:42:00.964 INFO  Funcotator - ------------------------------------------------------------
15:42:00.964 INFO  Funcotator - ------------------------------------------------------------
15:42:00.964 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:00.964 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:00.964 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:00.964 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:00.964 INFO  Funcotator - Deflater: IntelDeflater
15:42:00.964 INFO  Funcotator - Inflater: IntelInflater
15:42:00.964 INFO  Funcotator - GCS max retries/reopens: 20
15:42:00.964 INFO  Funcotator - Requester pays: disabled
15:42:00.964 INFO  Funcotator - Initializing engine
15:42:00.965 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
15:42:00.965 INFO  Funcotator - Done initializing engine
15:42:00.965 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:00.965 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:00.965 INFO  Funcotator - Initializing data sources...
15:42:00.965 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:00.965 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:00.966 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
15:42:00.966 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
15:42:00.966 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
15:42:00.966 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:00.966 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
15:42:00.966 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:00.966 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
15:42:00.967 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
15:42:00.967 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
15:42:00.967 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:00.967 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
15:42:00.968 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
15:42:00.969 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/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:42:00.970 INFO  Funcotator - Initializing Funcotator Engine...
15:42:00.970 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:00.970 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.
15:42:00.970 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:00.970 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2726346553281722236.vcf
15:42:00.971 INFO  ProgressMeter - Starting traversal
15:42:00.971 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:01.007 INFO  ProgressMeter -             unmapped              0.0                    57          95000.0
15:42:01.007 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:42:01.007 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:01.010 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:01.080 INFO  Funcotator - ------------------------------------------------------------
15:42:01.080 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:01.080 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:01.080 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:01.080 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:01.080 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:01 PM UTC
15:42:01.080 INFO  Funcotator - ------------------------------------------------------------
15:42:01.080 INFO  Funcotator - ------------------------------------------------------------
15:42:01.080 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:01.080 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:01.080 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:01.080 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:01.080 INFO  Funcotator - Deflater: IntelDeflater
15:42:01.080 INFO  Funcotator - Inflater: IntelInflater
15:42:01.080 INFO  Funcotator - GCS max retries/reopens: 20
15:42:01.080 INFO  Funcotator - Requester pays: disabled
15:42:01.080 INFO  Funcotator - Initializing engine
15:42:01.081 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
15:42:01.081 INFO  Funcotator - Done initializing engine
15:42:01.081 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:01.081 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:01.081 INFO  Funcotator - Initializing data sources...
15:42:01.081 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:01.081 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:01.081 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
15:42:01.081 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
15:42:01.081 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
15:42:01.082 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:01.082 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
15:42:01.082 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:01.082 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
15:42:01.082 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
15:42:01.083 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
15:42:01.083 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:01.083 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
15:42:01.084 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
15:42:01.085 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
15:42:01.086 INFO  Funcotator - Initializing Funcotator Engine...
15:42:01.086 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:01.086 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.
15:42:01.086 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:01.086 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17027197556441193534.maf
15:42:01.086 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
15:42:01.086 INFO  ProgressMeter - Starting traversal
15:42:01.086 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:01.089 WARN  MafOutputRenderer - 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=
15:42:01.089 WARN  MafOutputRenderer - 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=
15:42:01.089 WARN  MafOutputRenderer - 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=
15:42:01.090 WARN  MafOutputRenderer - 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=
15:42:01.091 WARN  MafOutputRenderer - 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=
15:42:01.091 WARN  MafOutputRenderer - 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=
15:42:01.092 WARN  MafOutputRenderer - 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=
15:42:01.092 WARN  MafOutputRenderer - 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=
15:42:01.093 WARN  MafOutputRenderer - 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=
15:42:01.093 WARN  MafOutputRenderer - 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=
15:42:01.093 WARN  MafOutputRenderer - 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=
15:42:01.094 WARN  MafOutputRenderer - 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=
15:42:01.094 WARN  MafOutputRenderer - 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=
15:42:01.095 WARN  MafOutputRenderer - 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=
15:42:01.096 WARN  MafOutputRenderer - 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=
15:42:01.096 WARN  MafOutputRenderer - 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=
15:42:01.097 WARN  MafOutputRenderer - 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=
15:42:01.097 WARN  MafOutputRenderer - 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=
15:42:01.097 WARN  MafOutputRenderer - 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=
15:42:01.098 WARN  MafOutputRenderer - 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=
15:42:01.099 WARN  MafOutputRenderer - 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=
15:42:01.099 WARN  MafOutputRenderer - 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=
15:42:01.101 WARN  MafOutputRenderer - 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=
15:42:01.101 WARN  MafOutputRenderer - 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=
15:42:01.101 WARN  MafOutputRenderer - 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=
15:42:01.103 WARN  MafOutputRenderer - 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=
15:42:01.103 WARN  MafOutputRenderer - 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=
15:42:01.104 WARN  MafOutputRenderer - 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=
15:42:01.105 WARN  MafOutputRenderer - 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=
15:42:01.105 WARN  MafOutputRenderer - 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=
15:42:01.105 WARN  MafOutputRenderer - 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=
15:42:01.107 WARN  MafOutputRenderer - 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=
15:42:01.107 WARN  MafOutputRenderer - 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=
15:42:01.107 WARN  MafOutputRenderer - 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=
15:42:01.108 WARN  MafOutputRenderer - 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=
15:42:01.109 WARN  MafOutputRenderer - 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=
15:42:01.109 WARN  MafOutputRenderer - 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=
15:42:01.111 WARN  MafOutputRenderer - 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=
15:42:01.111 WARN  MafOutputRenderer - 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=
15:42:01.111 WARN  MafOutputRenderer - 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=
15:42:01.112 WARN  MafOutputRenderer - 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=
15:42:01.113 WARN  MafOutputRenderer - 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=
15:42:01.113 WARN  MafOutputRenderer - 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=
15:42:01.114 WARN  MafOutputRenderer - 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=
15:42:01.114 WARN  MafOutputRenderer - 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=
15:42:01.115 WARN  MafOutputRenderer - 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=
15:42:01.116 WARN  MafOutputRenderer - 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=
15:42:01.116 WARN  MafOutputRenderer - 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=
15:42:01.116 WARN  MafOutputRenderer - 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=
15:42:01.118 WARN  MafOutputRenderer - 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=
15:42:01.118 WARN  MafOutputRenderer - 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=
15:42:01.118 WARN  MafOutputRenderer - 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=
15:42:01.119 WARN  MafOutputRenderer - 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=
15:42:01.120 WARN  MafOutputRenderer - 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=
15:42:01.120 WARN  MafOutputRenderer - 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=
15:42:01.120 WARN  MafOutputRenderer - 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=
15:42:01.121 WARN  MafOutputRenderer - 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=
15:42:01.121 INFO  ProgressMeter -             unmapped              0.0                    57          97714.3
15:42:01.121 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:42:01.121 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:01.121 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:01.122 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2726346553281722236.vcf
15:42:01.196 INFO  Funcotator - ------------------------------------------------------------
15:42:01.196 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:01.196 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:01.197 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:01.197 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:01.197 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:01 PM UTC
15:42:01.197 INFO  Funcotator - ------------------------------------------------------------
15:42:01.197 INFO  Funcotator - ------------------------------------------------------------
15:42:01.197 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:01.197 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:01.197 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:01.197 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:01.197 INFO  Funcotator - Deflater: IntelDeflater
15:42:01.197 INFO  Funcotator - Inflater: IntelInflater
15:42:01.197 INFO  Funcotator - GCS max retries/reopens: 20
15:42:01.197 INFO  Funcotator - Requester pays: disabled
15:42:01.197 INFO  Funcotator - Initializing engine
15:42:01.198 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
15:42:01.198 INFO  Funcotator - Done initializing engine
15:42:01.198 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:01.198 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:01.198 INFO  Funcotator - Initializing data sources...
15:42:01.198 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:42:01.199 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:01.199 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
15:42:01.199 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
15:42:01.199 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
15:42:01.199 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
15:42:01.200 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
15:42:01.200 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
15:42:01.200 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
15:42:01.200 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
15:42:01.200 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
15:42:01.200 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
15:42:01.200 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
15:42:01.201 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:01.201 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
15:42:01.201 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
15:42:01.201 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
15:42:01.201 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:01.201 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
15:42:01.202 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
15:42:01.246 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
15:42:01.265 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
15:42:01.273 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
15:42:01.273 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
15:42:01.273 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
15:42:01.274 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
15:42:01.892 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
15:42:01.930 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
15:42:01.930 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:01.931 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
15:42:01.931 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
15:42:02.014 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:42:02.014 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:02.014 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
15:42:02.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:02.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:42:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:42:02.042 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
15:42:02.042 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
15:42:02.043 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
15:42:02.043 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:42:02.044 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
15:42:02.046 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
15:42:02.048 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
15:42:02.050 INFO  Funcotator - Initializing Funcotator Engine...
15:42:02.050 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:02.050 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:42:02.050 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7206398643433019896.vcf
15:42:02.051 INFO  ProgressMeter - Starting traversal
15:42:02.051 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:17.926 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7559.1
15:42:18.396 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)
15:42:18.398 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)
15:42:19.152 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7217.1
15:42:19.152 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:42:19.152 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:42:19.154 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:19 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=3376414720
15:42:19.225 INFO  Funcotator - ------------------------------------------------------------
15:42:19.225 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:19.225 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:19.225 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:19.225 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:19.225 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:19 PM UTC
15:42:19.225 INFO  Funcotator - ------------------------------------------------------------
15:42:19.225 INFO  Funcotator - ------------------------------------------------------------
15:42:19.225 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:19.225 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:19.225 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:19.225 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:19.225 INFO  Funcotator - Deflater: IntelDeflater
15:42:19.225 INFO  Funcotator - Inflater: IntelInflater
15:42:19.225 INFO  Funcotator - GCS max retries/reopens: 20
15:42:19.225 INFO  Funcotator - Requester pays: disabled
15:42:19.225 INFO  Funcotator - Initializing engine
15:42:19.226 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
15:42:19.226 INFO  Funcotator - Done initializing engine
15:42:19.226 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:19.226 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:19.226 INFO  Funcotator - Initializing data sources...
15:42:19.226 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
15:42:19.226 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:19.227 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
15:42:19.227 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
15:42:19.227 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
15:42:19.227 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
15:42:19.227 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
15:42:19.227 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
15:42:19.227 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
15:42:19.228 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
15:42:19.228 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
15:42:19.228 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
15:42:19.228 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
15:42:19.228 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:19.228 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
15:42:19.228 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
15:42:19.228 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
15:42:19.228 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:19.229 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
15:42:19.229 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
15:42:19.273 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
15:42:19.292 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
15:42:19.300 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
15:42:19.300 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
15:42:19.300 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
15:42:19.300 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
15:42:19.923 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
15:42:19.963 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
15:42:19.963 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:19.964 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
15:42:19.964 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
15:42:20.049 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:42:20.049 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:20.050 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
15:42:20.077 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:42:20.077 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:42:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:42:20.077 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
15:42:20.078 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
15:42:20.078 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
15:42:20.078 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:42:20.079 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
15:42:20.081 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
15:42:20.084 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
15:42:20.086 INFO  Funcotator - Initializing Funcotator Engine...
15:42:20.086 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:20.086 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:42:20.086 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out2656190183109784896.maf
15:42:20.086 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
15:42:20.087 INFO  ProgressMeter - Starting traversal
15:42:20.087 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:35.835 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7620.0
15:42:36.308 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)
15:42:36.309 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)
15:42:37.058 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7272.4
15:42:37.058 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:42:37.058 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:42:37.059 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=3376414720
15:42:37.060 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7206398643433019896.vcf
15:42:37.432 INFO  Funcotator - ------------------------------------------------------------
15:42:37.432 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:37.432 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:37.432 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:37.432 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:37.432 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:37 PM UTC
15:42:37.432 INFO  Funcotator - ------------------------------------------------------------
15:42:37.432 INFO  Funcotator - ------------------------------------------------------------
15:42:37.432 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:37.432 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:37.432 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:37.432 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:37.432 INFO  Funcotator - Deflater: IntelDeflater
15:42:37.432 INFO  Funcotator - Inflater: IntelInflater
15:42:37.432 INFO  Funcotator - GCS max retries/reopens: 20
15:42:37.432 INFO  Funcotator - Requester pays: disabled
15:42:37.432 INFO  Funcotator - Initializing engine
15:42:37.433 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
15:42:37.450 INFO  Funcotator - Done initializing engine
15:42:37.450 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:37.450 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:37.450 INFO  Funcotator - Initializing data sources...
15:42:37.450 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:37.450 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:37.450 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
15:42:37.450 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
15:42:37.450 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
15:42:37.450 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:37.450 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
15:42:37.450 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:37.451 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
15:42:37.451 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
15:42:37.451 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
15:42:37.451 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:37.452 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
15:42:37.459 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
15:42:37.467 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
15:42:37.483 INFO  Funcotator - Initializing Funcotator Engine...
15:42:37.489 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:42:37.489 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3422591229811693084.vcf
15:42:37.500 INFO  ProgressMeter - Starting traversal
15:42:37.500 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:37.524 INFO  ProgressMeter -             unmapped              0.0                   100         250000.0
15:42:37.524 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:42:37.524 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:37.529 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:37.594 INFO  Funcotator - ------------------------------------------------------------
15:42:37.594 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:37.594 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:37.594 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:37.594 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:37.594 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:37 PM UTC
15:42:37.594 INFO  Funcotator - ------------------------------------------------------------
15:42:37.594 INFO  Funcotator - ------------------------------------------------------------
15:42:37.594 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:37.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:37.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:37.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:37.594 INFO  Funcotator - Deflater: IntelDeflater
15:42:37.594 INFO  Funcotator - Inflater: IntelInflater
15:42:37.594 INFO  Funcotator - GCS max retries/reopens: 20
15:42:37.594 INFO  Funcotator - Requester pays: disabled
15:42:37.594 INFO  Funcotator - Initializing engine
15:42:37.595 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
15:42:37.611 INFO  Funcotator - Done initializing engine
15:42:37.611 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:37.611 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:37.611 INFO  Funcotator - Initializing data sources...
15:42:37.611 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:37.611 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:37.611 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
15:42:37.611 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
15:42:37.611 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
15:42:37.611 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:37.611 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
15:42:37.611 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:37.612 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
15:42:37.612 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
15:42:37.613 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
15:42:37.613 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:37.613 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
15:42:37.621 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
15:42:37.629 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
15:42:37.636 INFO  Funcotator - Initializing Funcotator Engine...
15:42:37.640 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:42:37.640 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8498811085807681434.maf
15:42:37.641 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
15:42:37.641 INFO  ProgressMeter - Starting traversal
15:42:37.641 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:37.644 WARN  MafOutputRenderer - 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=
15:42:37.648 WARN  MafOutputRenderer - 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=
15:42:37.649 WARN  MafOutputRenderer - 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+
15:42:37.649 WARN  MafOutputRenderer - 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+
15:42:37.649 WARN  MafOutputRenderer - 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+
15:42:37.649 WARN  MafOutputRenderer - 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+
15:42:37.649 WARN  MafOutputRenderer - 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=
15:42:37.650 WARN  MafOutputRenderer - 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=
15:42:37.650 WARN  MafOutputRenderer - 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=
15:42:37.650 WARN  MafOutputRenderer - 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=
15:42:37.651 WARN  MafOutputRenderer - 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=
15:42:37.651 WARN  MafOutputRenderer - 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=
15:42:37.651 WARN  MafOutputRenderer - 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=
15:42:37.651 WARN  MafOutputRenderer - 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=
15:42:37.652 WARN  MafOutputRenderer - 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=
15:42:37.652 WARN  MafOutputRenderer - 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=
15:42:37.652 WARN  MafOutputRenderer - 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=
15:42:37.652 WARN  MafOutputRenderer - 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=
15:42:37.653 WARN  MafOutputRenderer - 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=
15:42:37.653 WARN  MafOutputRenderer - 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+
15:42:37.653 WARN  MafOutputRenderer - 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
15:42:37.653 WARN  MafOutputRenderer - 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=
15:42:37.654 WARN  MafOutputRenderer - 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=
15:42:37.654 WARN  MafOutputRenderer - 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=
15:42:37.654 WARN  MafOutputRenderer - 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=
15:42:37.654 WARN  MafOutputRenderer - 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=
15:42:37.654 WARN  MafOutputRenderer - 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=
15:42:37.655 WARN  MafOutputRenderer - 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=
15:42:37.655 WARN  MafOutputRenderer - 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
15:42:37.655 WARN  MafOutputRenderer - 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=
15:42:37.655 WARN  MafOutputRenderer - 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=
15:42:37.656 WARN  MafOutputRenderer - 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=
15:42:37.656 WARN  MafOutputRenderer - 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=
15:42:37.656 WARN  MafOutputRenderer - 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=
15:42:37.656 WARN  MafOutputRenderer - 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=
15:42:37.656 WARN  MafOutputRenderer - 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=
15:42:37.657 WARN  MafOutputRenderer - 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=
15:42:37.657 WARN  MafOutputRenderer - 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=
15:42:37.657 WARN  MafOutputRenderer - 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=
15:42:37.657 WARN  MafOutputRenderer - 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=
15:42:37.657 WARN  MafOutputRenderer - 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=
15:42:37.658 WARN  MafOutputRenderer - 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=
15:42:37.659 WARN  MafOutputRenderer - 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=
15:42:37.659 WARN  MafOutputRenderer - 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=
15:42:37.659 WARN  MafOutputRenderer - 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=
15:42:37.659 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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+
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.660 WARN  MafOutputRenderer - 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=
15:42:37.661 WARN  MafOutputRenderer - 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=
15:42:37.661 WARN  MafOutputRenderer - 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=
15:42:37.661 WARN  MafOutputRenderer - 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=
15:42:37.661 WARN  MafOutputRenderer - 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=
15:42:37.661 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.662 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.663 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.664 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.665 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.666 WARN  MafOutputRenderer - 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=
15:42:37.667 WARN  MafOutputRenderer - 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=
15:42:37.667 WARN  MafOutputRenderer - 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=
15:42:37.667 WARN  MafOutputRenderer - 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=
15:42:37.667 WARN  MafOutputRenderer - 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=
15:42:37.667 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.668 WARN  MafOutputRenderer - 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=
15:42:37.669 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
15:42:37.669 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:42:37.669 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:37.669 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:37.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3422591229811693084.vcf
15:42:37.796 INFO  Funcotator - ------------------------------------------------------------
15:42:37.796 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:37.796 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:37.796 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:37.796 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:37.796 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:37 PM UTC
15:42:37.796 INFO  Funcotator - ------------------------------------------------------------
15:42:37.796 INFO  Funcotator - ------------------------------------------------------------
15:42:37.796 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:37.796 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:37.796 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:37.796 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:37.796 INFO  Funcotator - Deflater: IntelDeflater
15:42:37.796 INFO  Funcotator - Inflater: IntelInflater
15:42:37.796 INFO  Funcotator - GCS max retries/reopens: 20
15:42:37.796 INFO  Funcotator - Requester pays: disabled
15:42:37.796 INFO  Funcotator - Initializing engine
15:42:37.797 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
15:42:37.797 INFO  Funcotator - Done initializing engine
15:42:37.797 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:37.797 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:37.797 INFO  Funcotator - Initializing data sources...
15:42:37.797 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:37.797 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:37.797 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
15:42:37.798 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
15:42:37.798 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
15:42:37.798 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:37.798 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
15:42:37.798 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:37.798 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
15:42:37.798 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
15:42:37.799 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
15:42:37.799 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:37.799 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
15:42:37.800 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
15:42:37.801 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
15:42:37.802 INFO  Funcotator - Initializing Funcotator Engine...
15:42:37.802 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:37.802 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.
15:42:37.802 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:37.802 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8200797966024020441.vcf
15:42:37.802 INFO  ProgressMeter - Starting traversal
15:42:37.802 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:37.832 INFO  ProgressMeter -             unmapped              0.0                    57         117931.0
15:42:37.832 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:42:37.832 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:37.834 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:37.899 INFO  Funcotator - ------------------------------------------------------------
15:42:37.899 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:37.899 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:37.899 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:37.899 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:37.899 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:37 PM UTC
15:42:37.899 INFO  Funcotator - ------------------------------------------------------------
15:42:37.899 INFO  Funcotator - ------------------------------------------------------------
15:42:37.899 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:37.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:37.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:37.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:37.899 INFO  Funcotator - Deflater: IntelDeflater
15:42:37.899 INFO  Funcotator - Inflater: IntelInflater
15:42:37.899 INFO  Funcotator - GCS max retries/reopens: 20
15:42:37.899 INFO  Funcotator - Requester pays: disabled
15:42:37.899 INFO  Funcotator - Initializing engine
15:42:37.900 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
15:42:37.900 INFO  Funcotator - Done initializing engine
15:42:37.900 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:37.900 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:37.900 INFO  Funcotator - Initializing data sources...
15:42:37.900 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:37.900 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:37.901 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
15:42:37.901 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
15:42:37.901 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
15:42:37.901 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:37.901 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
15:42:37.901 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:37.901 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
15:42:37.902 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
15:42:37.902 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
15:42:37.902 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:37.902 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
15:42:37.903 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
15:42:37.904 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
15:42:37.905 INFO  Funcotator - Initializing Funcotator Engine...
15:42:37.905 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:37.905 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.
15:42:37.905 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:42:37.905 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6774566997052898620.maf
15:42:37.905 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
15:42:37.905 INFO  ProgressMeter - Starting traversal
15:42:37.905 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:37.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
15:42:37.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
15:42:37.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
15:42:37.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:42:37.910 WARN  MafOutputRenderer - 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=
15:42:37.910 WARN  MafOutputRenderer - 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=
15:42:37.910 WARN  MafOutputRenderer - 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=
15:42:37.911 WARN  MafOutputRenderer - 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=
15:42:37.911 WARN  MafOutputRenderer - 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=
15:42:37.912 WARN  MafOutputRenderer - 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=
15:42:37.912 WARN  MafOutputRenderer - 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=
15:42:37.912 WARN  MafOutputRenderer - 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=
15:42:37.913 WARN  MafOutputRenderer - 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=
15:42:37.914 WARN  MafOutputRenderer - 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=
15:42:37.914 WARN  MafOutputRenderer - 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=
15:42:37.915 WARN  MafOutputRenderer - 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=
15:42:37.915 WARN  MafOutputRenderer - 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=
15:42:37.916 WARN  MafOutputRenderer - 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=
15:42:37.916 WARN  MafOutputRenderer - 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=
15:42:37.916 WARN  MafOutputRenderer - 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=
15:42:37.918 WARN  MafOutputRenderer - 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=
15:42:37.918 WARN  MafOutputRenderer - 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=
15:42:37.919 WARN  MafOutputRenderer - 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=
15:42:37.920 WARN  MafOutputRenderer - 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=
15:42:37.920 WARN  MafOutputRenderer - 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=
15:42:37.921 WARN  MafOutputRenderer - 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=
15:42:37.921 WARN  MafOutputRenderer - 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=
15:42:37.923 WARN  MafOutputRenderer - 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=
15:42:37.923 WARN  MafOutputRenderer - 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=
15:42:37.923 WARN  MafOutputRenderer - 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=
15:42:37.924 WARN  MafOutputRenderer - 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=
15:42:37.925 WARN  MafOutputRenderer - 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=
15:42:37.925 WARN  MafOutputRenderer - 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=
15:42:37.926 WARN  MafOutputRenderer - 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=
15:42:37.926 WARN  MafOutputRenderer - 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=
15:42:37.927 WARN  MafOutputRenderer - 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=
15:42:37.927 WARN  MafOutputRenderer - 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=
15:42:37.929 WARN  MafOutputRenderer - 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=
15:42:37.929 WARN  MafOutputRenderer - 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=
15:42:37.929 WARN  MafOutputRenderer - 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=
15:42:37.930 WARN  MafOutputRenderer - 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=
15:42:37.931 WARN  MafOutputRenderer - 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=
15:42:37.931 WARN  MafOutputRenderer - 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=
15:42:37.932 WARN  MafOutputRenderer - 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=
15:42:37.932 WARN  MafOutputRenderer - 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=
15:42:37.933 WARN  MafOutputRenderer - 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=
15:42:37.934 WARN  MafOutputRenderer - 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=
15:42:37.934 WARN  MafOutputRenderer - 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=
15:42:37.934 WARN  MafOutputRenderer - 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=
15:42:37.935 WARN  MafOutputRenderer - 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=
15:42:37.936 WARN  MafOutputRenderer - 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=
15:42:37.936 WARN  MafOutputRenderer - 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=
15:42:37.936 WARN  MafOutputRenderer - 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=
15:42:37.938 WARN  MafOutputRenderer - 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=
15:42:37.938 WARN  MafOutputRenderer - 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=
15:42:37.938 WARN  MafOutputRenderer - 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=
15:42:37.939 WARN  MafOutputRenderer - 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=
15:42:37.939 INFO  ProgressMeter -             unmapped              0.0                    57         100588.2
15:42:37.939 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:42:37.939 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:42:37.939 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:37 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:37.940 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8200797966024020441.vcf
15:42:38.033 INFO  Funcotator - ------------------------------------------------------------
15:42:38.033 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:38.033 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:38.033 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:38.033 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:38.033 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:38 PM UTC
15:42:38.033 INFO  Funcotator - ------------------------------------------------------------
15:42:38.033 INFO  Funcotator - ------------------------------------------------------------
15:42:38.033 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:38.033 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:38.033 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:38.034 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:38.034 INFO  Funcotator - Deflater: IntelDeflater
15:42:38.034 INFO  Funcotator - Inflater: IntelInflater
15:42:38.034 INFO  Funcotator - GCS max retries/reopens: 20
15:42:38.034 INFO  Funcotator - Requester pays: disabled
15:42:38.034 INFO  Funcotator - Initializing engine
15:42:38.034 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
15:42:38.035 INFO  Funcotator - Done initializing engine
15:42:38.035 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:38.035 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:38.036 INFO  Funcotator - Initializing data sources...
15:42:38.036 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
15:42:38.036 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:38.036 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
15:42:38.036 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
15:42:38.036 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
15:42:38.036 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:38.036 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
15:42:38.036 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:38.037 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
15:42:38.037 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
15:42:38.037 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
15:42:38.037 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:42:38.038 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
15:42:38.038 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
15:42:38.040 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
15:42:38.040 INFO  Funcotator - Initializing Funcotator Engine...
15:42:38.040 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:38.040 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.
15:42:38.040 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14972600950124701797.maf
15:42:38.041 INFO  ProgressMeter - Starting traversal
15:42:38.041 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:38.043 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 @ 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=
15:42:38.044 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 @ 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=
15:42:38.045 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 @ 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=
15:42:38.045 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 @ 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=
15:42:38.046 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 @ 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=
15:42:38.046 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 @ 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=
15:42:38.047 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 @ 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=
15:42:38.047 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 @ 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=
15:42:38.047 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 @ 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=
15:42:38.048 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 @ 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=
15:42:38.048 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 @ 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=
15:42:38.048 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 @ 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=
15:42:38.049 WARN  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=
15:42:38.049 WARN  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=
15:42:38.049 WARN  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=
15:42:38.049 WARN  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=
15:42:38.050 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 @ 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=
15:42:38.050 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 @ 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=
15:42:38.050 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 @ 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=
15:42:38.050 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 @ 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=
15:42:38.051 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 @ 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=
15:42:38.051 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
15:42:38.051 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:42:38.051 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:42:38.051 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:38 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:38.125 INFO  Funcotator - ------------------------------------------------------------
15:42:38.125 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:38.125 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:38.125 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:38.125 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:38.125 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:38 PM UTC
15:42:38.125 INFO  Funcotator - ------------------------------------------------------------
15:42:38.125 INFO  Funcotator - ------------------------------------------------------------
15:42:38.125 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:38.125 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:38.125 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:38.125 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:38.125 INFO  Funcotator - Deflater: IntelDeflater
15:42:38.125 INFO  Funcotator - Inflater: IntelInflater
15:42:38.125 INFO  Funcotator - GCS max retries/reopens: 20
15:42:38.125 INFO  Funcotator - Requester pays: disabled
15:42:38.125 INFO  Funcotator - Initializing engine
15:42:38.126 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
15:42:38.127 INFO  Funcotator - Done initializing engine
15:42:38.127 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:38.127 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:38.127 INFO  Funcotator - Initializing data sources...
15:42:38.127 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:42:38.127 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:38.127 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
15:42:38.127 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
15:42:38.127 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
15:42:38.127 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:38.128 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:42:38.128 INFO  DataSourceUtils - Resolved 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
15:42:38.128 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
15:42:38.156 INFO  DataSourceUtils - Resolved 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
15:42:38.156 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:42:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:42:38.157 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
15:42:38.157 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:38.157 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
15:42:38.158 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
15:42:38.158 INFO  Funcotator - Initializing Funcotator Engine...
15:42:38.158 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:38.158 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.
15:42:38.158 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3800510162467831996.vcf
15:42:38.162 INFO  ProgressMeter - Starting traversal
15:42:38.162 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:38.165 INFO  ProgressMeter -             unmapped              0.0                    10         200000.0
15:42:38.166 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:42:38.166 WARN  Funcotator - ================================================================================
15:42:38.166 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:42:38.166 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:42:38.166 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:42:38.166 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:42:38.166 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:42:38.166 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:42:38.166 WARN  Funcotator - --------------------------------------------------------------------------------
15:42:38.166 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:42:38.166 WARN  Funcotator -  run was misconfigured.     
15:42:38.166 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:42:38.166 WARN  Funcotator - ================================================================================
15:42:38.166 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:38 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:38.167 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3800510162467831996.vcf
15:42:38.237 INFO  Funcotator - ------------------------------------------------------------
15:42:38.237 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:42:38.237 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:38.237 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:42:38.237 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:42:38.237 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:42:38 PM UTC
15:42:38.237 INFO  Funcotator - ------------------------------------------------------------
15:42:38.237 INFO  Funcotator - ------------------------------------------------------------
15:42:38.237 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:38.237 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:38.237 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:38.237 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:38.237 INFO  Funcotator - Deflater: IntelDeflater
15:42:38.237 INFO  Funcotator - Inflater: IntelInflater
15:42:38.237 INFO  Funcotator - GCS max retries/reopens: 20
15:42:38.237 INFO  Funcotator - Requester pays: disabled
15:42:38.237 INFO  Funcotator - Initializing engine
15:42:38.238 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
15:42:38.240 INFO  Funcotator - Done initializing engine
15:42:38.240 INFO  Funcotator - Skipping sequence dictionary validation.
15:42:38.240 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:42:38.240 INFO  Funcotator - Initializing data sources...
15:42:38.240 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:42:38.240 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:42:38.240 INFO  DataSourceUtils - Resolved 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
15:42:38.240 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
15:42:38.240 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
15:42:38.240 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:42:38.240 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:42:38.240 INFO  DataSourceUtils - Resolved 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
15:42:38.241 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
15:42:38.277 INFO  DataSourceUtils - Resolved 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
15:42:38.277 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:42:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:42:38.278 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
15:42:38.278 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:42:38.278 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
15:42:38.279 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
15:42:38.279 INFO  Funcotator - Initializing Funcotator Engine...
15:42:38.279 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:42:38.279 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.
15:42:38.279 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13174712317064155838.vcf
15:42:38.282 INFO  ProgressMeter - Starting traversal
15:42:38.283 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:42:38.284 INFO  ProgressMeter -             unmapped              0.0                     1          60000.0
15:42:38.284 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:42:38.284 WARN  Funcotator - ================================================================================
15:42:38.284 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:42:38.284 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:42:38.284 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:42:38.284 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:42:38.284 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:42:38.284 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:42:38.284 WARN  Funcotator - --------------------------------------------------------------------------------
15:42:38.284 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:42:38.284 WARN  Funcotator -  run was misconfigured.     
15:42:38.284 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:42:38.284 WARN  Funcotator - ================================================================================
15:42:38.285 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:42:38 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3376414720
15:42:38.286 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13174712317064155838.vcf