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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
tests
failures
ignored
1m40.50s
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/funcotatorTmpFolder6985394976696690958/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)	1.095s	passed
exhaustiveArgumentTest[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.274s	passed
exhaustiveArgumentTest[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	1.092s	passed
exhaustiveArgumentTest[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.045s	passed
exhaustiveArgumentTest[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	0.964s	passed
exhaustiveArgumentTest[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.155s	passed
exhaustiveArgumentTest[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	0.952s	passed
exhaustiveArgumentTest[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.150s	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)	6.474s	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)	5.586s	passed
nonTrivialLargeDataValidationTest[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false)	1.812s	passed
nonTrivialLargeDataValidationTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, hg38, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf, [], false)	1.795s	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)	12.731s	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)	5.835s	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	0.183s	passed
testCanAnnotateMixedContigHg19Clinvar	0.098s	passed
testCanAnnotateSpanningDeletions	0.184s	passed
testCanCreateNonLocatableFuncotations	0.976s	passed
testCanHandleSymbollicAlleleFuncotations	1.038s	passed
testCustomVariantClassificationOrder	1.050s	passed
testEColiFuncotations	0.098s	passed
testEnsureDbSnpInMaf	0.083s	passed
testExclusionFromDatasourceVcfToVcf	0.218s	passed
testFilterParsing	0.108s	passed
testFuncotatorWithoutValidatingResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	1.035s	passed
testFuncotatorWithoutValidatingResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.006s	passed
testFuncotatorWithoutValidatingResults[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	0.925s	passed
testFuncotatorWithoutValidatingResults[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	0.982s	passed
testFuncotatorWithoutValidatingResults[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	0.893s	passed
testFuncotatorWithoutValidatingResults[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.034s	passed
testFuncotatorWithoutValidatingResults[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6985394976696690958/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)	0.935s	passed
testFuncotatorWithoutValidatingResults[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8638647909576018639/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)	1.027s	passed
testMANESelectAnnotationDifferencesAndGencodeV43	0.336s	passed
testMafCustomCountFieldsTumorOnly[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf)	0.083s	passed
testMafCustomCountFieldsTumorOnly[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf)	0.082s	passed
testMafCustomCountFields[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf)	0.139s	passed
testMafCustomCountFields[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf)	0.082s	passed
testManualAnnotationsCorrectness	0.102s	passed
testMoreThanOneTNPair	0.075s	passed
testNoSpanningDeletionWriteWithMAF	0.130s	passed
testNoVariantsProduceMaf	0.071s	passed
testSequenceDictionaryCheck	0.066s	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)	5.872s	passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput	0.892s	passed
testVCFColumnsArentShuffled	0.079s	passed
testVCFToMAFPreservesFields	0.090s	passed
testVCFToVCFPreservesFields	0.093s	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/funcotatorTmpFolder17496126976990019662/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15)	0.172s	passed
testVcfMafConcordance[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder17496126976990019662/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.223s	passed
testVcfMafConcordance[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder8638647909576018639/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057)	36.000s	passed
testVcfMafConcordance[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder5981625768438900241/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)	0.359s	passed
testVcfMafConcordance[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder17496126976990019662/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)	0.251s	passed
testVcfToMafHonorsExcludedFields	0.090s	passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified	0.111s	passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations	0.107s	passed
Standard error

13:45:07.450 INFO  Funcotator - ------------------------------------------------------------
13:45:07.450 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:07.450 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:07.450 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:07.450 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:07.450 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:07 PM UTC
13:45:07.450 INFO  Funcotator - ------------------------------------------------------------
13:45:07.450 INFO  Funcotator - ------------------------------------------------------------
13:45:07.451 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:07.451 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:07.451 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:07.451 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:07.451 INFO  Funcotator - Deflater: IntelDeflater
13:45:07.451 INFO  Funcotator - Inflater: IntelInflater
13:45:07.451 INFO  Funcotator - GCS max retries/reopens: 20
13:45:07.451 INFO  Funcotator - Requester pays: disabled
13:45:07.451 INFO  Funcotator - Initializing engine
13:45:07.452 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
13:45:07.453 INFO  Funcotator - Done initializing engine
13:45:07.453 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:07.453 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:07.453 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder941265435396167344/TranscriptIdFile.txt
13:45:07.453 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
13:45:07.454 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:07.454 INFO  Funcotator - Initializing data sources...
13:45:07.454 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:07.454 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:07.454 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:07.454 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
13:45:07.455 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
13:45:07.455 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
13:45:07.455 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
13:45:07.455 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
13:45:07.456 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
13:45:07.456 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
13:45:07.456 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
13:45:07.456 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
13:45:07.456 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
13:45:07.457 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:07.457 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
13:45:07.457 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
13:45:07.457 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:07.457 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:07.458 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
13:45:07.538 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
13:45:07.581 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
13:45:07.599 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
13:45:07.605 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
13:45:07.606 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
13:45:07.606 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
13:45:07.607 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
13:45:08.186 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
13:45:08.224 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
13:45:08.224 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:08.225 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
13:45:08.225 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
13:45:08.358 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:08.358 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:08.359 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
13:45:08.386 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:08.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:08.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:08.388 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
13:45:08.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:08.389 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:08.389 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
13:45:08.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:08.396 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
13:45:08.400 INFO  Funcotator - Initializing Funcotator Engine...
13:45:08.400 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
13:45:08.400 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:08.400 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:08.401 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:08.401 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:08.402 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:08.403 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:08.403 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:08.403 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.317286456063604802343.vcf
13:45:08.404 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
13:45:08.406 INFO  ProgressMeter - Starting traversal
13:45:08.406 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:08.474 INFO  ProgressMeter -             unmapped              0.0                     3           2647.1
13:45:08.474 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:08.475 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:08.477 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:08 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1939865600
13:45:08.547 INFO  Funcotator - ------------------------------------------------------------
13:45:08.547 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:08.547 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:08.547 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:08.547 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:08.547 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:08 PM UTC
13:45:08.547 INFO  Funcotator - ------------------------------------------------------------
13:45:08.547 INFO  Funcotator - ------------------------------------------------------------
13:45:08.547 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:08.547 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:08.547 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:08.547 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:08.548 INFO  Funcotator - Deflater: IntelDeflater
13:45:08.548 INFO  Funcotator - Inflater: IntelInflater
13:45:08.548 INFO  Funcotator - GCS max retries/reopens: 20
13:45:08.548 INFO  Funcotator - Requester pays: disabled
13:45:08.548 INFO  Funcotator - Initializing engine
13:45:08.549 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
13:45:08.550 INFO  Funcotator - Done initializing engine
13:45:08.550 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:08.550 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:08.550 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder18348931819764886266/TranscriptIdFile.txt
13:45:08.550 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
13:45:08.550 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:08.550 INFO  Funcotator - Initializing data sources...
13:45:08.550 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:08.550 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:08.551 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
13:45:08.551 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
13:45:08.551 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
13:45:08.552 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
13:45:08.552 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
13:45:08.552 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
13:45:08.552 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
13:45:08.553 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
13:45:08.553 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
13:45:08.553 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
13:45:08.553 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
13:45:08.553 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:08.554 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
13:45:08.554 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
13:45:08.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:08.554 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:08.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:08.555 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
13:45:08.625 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
13:45:08.655 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
13:45:08.663 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
13:45:08.664 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
13:45:08.664 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
13:45:08.664 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
13:45:09.369 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
13:45:09.407 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
13:45:09.407 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:09.408 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
13:45:09.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:45:09.494 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:09.495 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:09.495 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
13:45:09.522 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:09.522 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:09	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:09.522 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
13:45:09.523 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
13:45:09.523 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
13:45:09.523 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:09.524 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
13:45:09.527 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:09.531 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:09.534 INFO  Funcotator - Initializing Funcotator Engine...
13:45:09.534 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:09.534 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:09.534 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.417793210292929234864.vcf
13:45:09.535 INFO  ProgressMeter - Starting traversal
13:45:09.535 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:09.751 INFO  ProgressMeter -             unmapped              0.0                     4           1111.1
13:45:09.751 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:09.751 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:09.752 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2009071616
13:45:09.825 INFO  Funcotator - ------------------------------------------------------------
13:45:09.825 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:09.825 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:09.825 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:09.825 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:09.825 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:09 PM UTC
13:45:09.825 INFO  Funcotator - ------------------------------------------------------------
13:45:09.825 INFO  Funcotator - ------------------------------------------------------------
13:45:09.825 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:09.825 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:09.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:09.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:09.826 INFO  Funcotator - Deflater: IntelDeflater
13:45:09.826 INFO  Funcotator - Inflater: IntelInflater
13:45:09.826 INFO  Funcotator - GCS max retries/reopens: 20
13:45:09.826 INFO  Funcotator - Requester pays: disabled
13:45:09.826 INFO  Funcotator - Initializing engine
13:45:09.826 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
13:45:09.827 INFO  Funcotator - Done initializing engine
13:45:09.827 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:09.827 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:09.827 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6043016096741926209/TranscriptIdFile.txt
13:45:09.827 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
13:45:09.827 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:09.827 INFO  Funcotator - Initializing data sources...
13:45:09.827 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:09.827 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:09.828 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
13:45:09.828 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
13:45:09.828 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
13:45:09.829 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
13:45:09.829 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
13:45:09.829 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
13:45:09.829 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
13:45:09.829 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
13:45:09.830 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
13:45:09.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:09.830 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
13:45:09.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:09.830 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
13:45:09.830 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
13:45:09.831 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:09.831 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:09.831 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
13:45:09.831 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
13:45:09.874 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
13:45:09.893 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
13:45:09.900 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
13:45:09.900 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:45:09.901 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
13:45:09.901 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
13:45:10.574 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
13:45:10.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:10.632 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:10.633 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:10.634 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
13:45:10.742 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:10.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:10.743 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
13:45:10.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:10.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:45:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:10.788 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:10.789 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
13:45:10.790 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:10.790 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:10.791 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
13:45:10.795 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:10.800 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
13:45:10.804 INFO  Funcotator - Initializing Funcotator Engine...
13:45:10.804 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
13:45:10.804 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:10.804 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:10.804 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:10.804 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:10.805 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:10.805 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:10.805 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.314108171685606113270.vcf
13:45:10.805 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
13:45:10.807 INFO  ProgressMeter - Starting traversal
13:45:10.807 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:10.841 INFO  ProgressMeter -             unmapped              0.0                     3           5294.1
13:45:10.841 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:10.841 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:10.844 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2325741568
13:45:10.911 INFO  Funcotator - ------------------------------------------------------------
13:45:10.911 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:10.911 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:10.911 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:10.912 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:10.912 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:10 PM UTC
13:45:10.912 INFO  Funcotator - ------------------------------------------------------------
13:45:10.912 INFO  Funcotator - ------------------------------------------------------------
13:45:10.912 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:10.912 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:10.912 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:10.912 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:10.912 INFO  Funcotator - Deflater: IntelDeflater
13:45:10.912 INFO  Funcotator - Inflater: IntelInflater
13:45:10.912 INFO  Funcotator - GCS max retries/reopens: 20
13:45:10.912 INFO  Funcotator - Requester pays: disabled
13:45:10.912 INFO  Funcotator - Initializing engine
13:45:10.913 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
13:45:10.913 INFO  Funcotator - Done initializing engine
13:45:10.913 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:10.913 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:10.913 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder931932087736631773/TranscriptIdFile.txt
13:45:10.913 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
13:45:10.914 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:10.914 INFO  Funcotator - Initializing data sources...
13:45:10.914 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:10.914 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:10.914 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
13:45:10.914 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
13:45:10.914 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
13:45:10.915 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
13:45:10.915 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
13:45:10.915 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
13:45:10.915 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
13:45:10.915 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
13:45:10.916 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
13:45:10.916 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
13:45:10.916 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
13:45:10.916 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:10.916 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
13:45:10.916 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
13:45:10.917 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:10.917 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:10.917 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
13:45:10.917 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
13:45:10.987 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
13:45:11.005 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
13:45:11.012 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
13:45:11.012 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
13:45:11.012 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
13:45:11.013 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
13:45:11.615 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
13:45:11.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:11.652 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:11.653 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
13:45:11.653 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
13:45:11.737 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:11.738 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
13:45:11.738 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
13:45:11.765 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:11.765 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:11.766 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
13:45:11.766 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
13:45:11.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:11.767 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:11.768 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:11.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:11.772 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
13:45:11.774 INFO  Funcotator - Initializing Funcotator Engine...
13:45:11.774 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:11.774 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:11.774 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.414429612898727021721.vcf
13:45:11.775 INFO  ProgressMeter - Starting traversal
13:45:11.775 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:11.888 INFO  ProgressMeter -             unmapped              0.0                     4           2123.9
13:45:11.889 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:11.889 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:11.889 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:11 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2325741568
13:45:11.955 INFO  Funcotator - ------------------------------------------------------------
13:45:11.955 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:11.955 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:11.955 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:11.955 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:11.955 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:11 PM UTC
13:45:11.955 INFO  Funcotator - ------------------------------------------------------------
13:45:11.955 INFO  Funcotator - ------------------------------------------------------------
13:45:11.955 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:11.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:11.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:11.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:11.955 INFO  Funcotator - Deflater: IntelDeflater
13:45:11.955 INFO  Funcotator - Inflater: IntelInflater
13:45:11.955 INFO  Funcotator - GCS max retries/reopens: 20
13:45:11.955 INFO  Funcotator - Requester pays: disabled
13:45:11.955 INFO  Funcotator - Initializing engine
13:45:11.956 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
13:45:11.957 INFO  Funcotator - Done initializing engine
13:45:11.957 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:11.957 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:11.957 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4203234825852474491/TranscriptIdFile.txt
13:45:11.957 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
13:45:11.957 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:11.957 INFO  Funcotator - Initializing data sources...
13:45:11.957 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:11.957 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:11.957 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
13:45:11.957 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
13:45:11.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:11.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
13:45:11.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:45:11.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:45:11.958 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
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:11.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:11.960 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:11.960 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:11.960 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:11.960 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:11.960 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
13:45:12.001 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
13:45:12.070 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
13:45:12.077 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
13:45:12.077 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
13:45:12.077 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
13:45:12.078 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
13:45:12.652 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
13:45:12.691 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
13:45:12.691 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:12.691 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
13:45:12.692 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
13:45:12.776 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:12.776 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:12.777 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
13:45:12.803 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:12.804 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:12.804 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
13:45:12.804 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
13:45:12.805 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
13:45:12.805 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:12.806 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
13:45:12.808 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:12.811 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
13:45:12.813 INFO  Funcotator - Initializing Funcotator Engine...
13:45:12.813 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
13:45:12.813 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:12.813 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:12.813 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:12.813 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:12.814 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:12.814 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:12.814 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.318438682752275738734.maf
13:45:12.816 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
13:45:12.818 INFO  ProgressMeter - Starting traversal
13:45:12.818 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:12.853 INFO  ProgressMeter -             unmapped              0.0                     3           5142.9
13:45:12.853 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:12.853 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:12.853 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:12 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2325741568
13:45:12.921 INFO  Funcotator - ------------------------------------------------------------
13:45:12.921 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:12.921 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:12.921 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:12.921 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:12.921 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:12 PM UTC
13:45:12.921 INFO  Funcotator - ------------------------------------------------------------
13:45:12.921 INFO  Funcotator - ------------------------------------------------------------
13:45:12.921 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:12.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:12.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:12.921 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:12.921 INFO  Funcotator - Deflater: IntelDeflater
13:45:12.921 INFO  Funcotator - Inflater: IntelInflater
13:45:12.921 INFO  Funcotator - GCS max retries/reopens: 20
13:45:12.921 INFO  Funcotator - Requester pays: disabled
13:45:12.921 INFO  Funcotator - Initializing engine
13:45:12.922 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
13:45:12.923 INFO  Funcotator - Done initializing engine
13:45:12.923 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:12.923 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:12.923 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4603053028057090519/TranscriptIdFile.txt
13:45:12.923 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
13:45:12.923 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:12.923 INFO  Funcotator - Initializing data sources...
13:45:12.923 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:12.923 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:12.923 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:12.923 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
13:45:12.924 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:12.924 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
13:45:12.924 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
13:45:12.924 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
13:45:12.924 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
13:45:12.924 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
13:45:12.925 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
13:45:12.925 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
13:45:12.925 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
13:45:12.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:12.925 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
13:45:12.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:12.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:12.925 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:12.925 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:12.926 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
13:45:12.969 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
13:45:12.987 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
13:45:12.994 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
13:45:12.994 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
13:45:12.994 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
13:45:12.995 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
13:45:13.671 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
13:45:13.708 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
13:45:13.708 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:13.709 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
13:45:13.709 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
13:45:13.805 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:13.805 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:13.806 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
13:45:13.832 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:13.833 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:13	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:13.833 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
13:45:13.833 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
13:45:13.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:13.834 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:13.835 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
13:45:13.837 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:13.839 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
13:45:13.841 INFO  Funcotator - Initializing Funcotator Engine...
13:45:13.841 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:13.841 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:13.841 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.44367338086060618285.maf
13:45:13.842 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
13:45:13.844 INFO  ProgressMeter - Starting traversal
13:45:13.844 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:14.008 INFO  ProgressMeter -             unmapped              0.0                     4           1463.4
13:45:14.008 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:14.008 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:14.008 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:14 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2457862144
13:45:14.073 INFO  Funcotator - ------------------------------------------------------------
13:45:14.073 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:14.073 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:14.073 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:14.073 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:14.073 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:14 PM UTC
13:45:14.073 INFO  Funcotator - ------------------------------------------------------------
13:45:14.073 INFO  Funcotator - ------------------------------------------------------------
13:45:14.073 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:14.073 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:14.073 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:14.073 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:14.073 INFO  Funcotator - Deflater: IntelDeflater
13:45:14.073 INFO  Funcotator - Inflater: IntelInflater
13:45:14.073 INFO  Funcotator - GCS max retries/reopens: 20
13:45:14.073 INFO  Funcotator - Requester pays: disabled
13:45:14.073 INFO  Funcotator - Initializing engine
13:45:14.074 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
13:45:14.075 INFO  Funcotator - Done initializing engine
13:45:14.075 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:14.075 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:14.075 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8434919027533053206/TranscriptIdFile.txt
13:45:14.075 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
13:45:14.075 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:14.075 INFO  Funcotator - Initializing data sources...
13:45:14.075 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:14.075 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:14.075 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
13:45:14.075 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
13:45:14.076 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
13:45:14.076 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
13:45:14.076 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
13:45:14.076 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
13:45:14.076 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
13:45:14.076 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
13:45:14.077 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
13:45:14.077 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
13:45:14.077 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
13:45:14.077 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
13:45:14.077 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
13:45:14.077 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
13:45:14.077 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:14.078 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:14.078 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
13:45:14.078 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
13:45:14.119 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:14.137 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
13:45:14.144 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
13:45:14.144 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
13:45:14.144 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
13:45:14.145 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
13:45:14.777 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
13:45:14.814 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
13:45:14.814 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:14.815 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
13:45:14.815 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
13:45:14.899 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:14.899 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
13:45:14.900 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
13:45:14.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:14.927 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:45:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:14.927 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
13:45:14.928 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:14.928 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:14.928 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:14.929 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:14.931 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:14.934 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
13:45:14.936 INFO  Funcotator - Initializing Funcotator Engine...
13:45:14.936 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
13:45:14.936 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:14.936 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:14.936 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:14.936 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:14.937 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:14.937 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:14.937 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.310919615547609576661.maf
13:45:14.937 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
13:45:14.939 INFO  ProgressMeter - Starting traversal
13:45:14.939 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:14.961 INFO  ProgressMeter -             unmapped              0.0                     3           8181.8
13:45:14.961 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:14.961 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:14.961 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:14 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2457862144
13:45:15.030 INFO  Funcotator - ------------------------------------------------------------
13:45:15.030 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:15.030 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:15.030 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:15.030 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:15.030 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:15 PM UTC
13:45:15.030 INFO  Funcotator - ------------------------------------------------------------
13:45:15.030 INFO  Funcotator - ------------------------------------------------------------
13:45:15.030 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:15.030 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:15.030 INFO  Funcotator - Deflater: IntelDeflater
13:45:15.030 INFO  Funcotator - Inflater: IntelInflater
13:45:15.030 INFO  Funcotator - GCS max retries/reopens: 20
13:45:15.030 INFO  Funcotator - Requester pays: disabled
13:45:15.030 INFO  Funcotator - Initializing engine
13:45:15.031 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
13:45:15.032 INFO  Funcotator - Done initializing engine
13:45:15.032 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:15.032 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:15.032 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder1051361623532322097/TranscriptIdFile.txt
13:45:15.032 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
13:45:15.032 INFO  FuncotatorEngine - Transcript parsing complete.
13:45:15.032 INFO  Funcotator - Initializing data sources...
13:45:15.032 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:15.032 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:15.032 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
13:45:15.033 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
13:45:15.033 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
13:45:15.033 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
13:45:15.033 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
13:45:15.033 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
13:45:15.033 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
13:45:15.034 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
13:45:15.034 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
13:45:15.034 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
13:45:15.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:45:15.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:15.034 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
13:45:15.034 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
13:45:15.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:15.035 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:15.035 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
13:45:15.035 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
13:45:15.147 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
13:45:15.176 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
13:45:15.189 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
13:45:15.189 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
13:45:15.189 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
13:45:15.190 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
13:45:15.812 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
13:45:15.851 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
13:45:15.851 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:15.852 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
13:45:15.852 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
13:45:15.957 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:15.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:15.958 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
13:45:15.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:15.986 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:15.986 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
13:45:15.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:15.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:15.987 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:15.988 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
13:45:15.990 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
13:45:15.993 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
13:45:15.995 INFO  Funcotator - Initializing Funcotator Engine...
13:45:15.995 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:15.995 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:15.995 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.415866173550508478415.maf
13:45:15.995 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
13:45:15.997 INFO  ProgressMeter - Starting traversal
13:45:15.997 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:16.111 INFO  ProgressMeter -             unmapped              0.0                     4           2105.3
13:45:16.111 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:16.111 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:16.111 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:16 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2608857088
13:45:16.195 INFO  Funcotator - ------------------------------------------------------------
13:45:16.195 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:16.195 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:16.195 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:16.195 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:16.195 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:16 PM UTC
13:45:16.195 INFO  Funcotator - ------------------------------------------------------------
13:45:16.195 INFO  Funcotator - ------------------------------------------------------------
13:45:16.195 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:16.195 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:16.195 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:16.195 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:16.195 INFO  Funcotator - Deflater: IntelDeflater
13:45:16.195 INFO  Funcotator - Inflater: IntelInflater
13:45:16.195 INFO  Funcotator - GCS max retries/reopens: 20
13:45:16.195 INFO  Funcotator - Requester pays: disabled
13:45:16.195 INFO  Funcotator - Initializing engine
13:45:16.198 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
13:45:16.199 INFO  Funcotator - Done initializing engine
13:45:16.199 INFO  Funcotator - Validating sequence dictionaries...
13:45:16.199 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:16.199 INFO  Funcotator - Initializing data sources...
13:45:16.199 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:16.199 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:16.199 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
13:45:16.200 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
13:45:16.200 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
13:45:16.200 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
13:45:16.200 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
13:45:16.200 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
13:45:16.200 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
13:45:16.200 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 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
13:45:16.201 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:16.201 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
13:45:16.202 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
13:45:16.243 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
13:45:16.325 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
13:45:16.332 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
13:45:16.332 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
13:45:16.332 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
13:45:16.332 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
13:45:17.077 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
13:45:17.115 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
13:45:17.115 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:17.116 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:17.116 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
13:45:17.203 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:17.203 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:17.204 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
13:45:17.233 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:17.233 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:17	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:17.234 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
13:45:17.234 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
13:45:17.234 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:17.234 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:17.235 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:17.237 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:17.240 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:17.242 INFO  Funcotator - Initializing Funcotator Engine...
13:45:17.242 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:17.242 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
13:45:17.242 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator2044347494396466169.vcf
13:45:17.244 INFO  ProgressMeter - Starting traversal
13:45:17.244 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:19.481 INFO  ProgressMeter -             unmapped              0.0                   198           5310.7
13:45:19.481 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:45:19.482 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:45:19.490 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:19 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2785017856
13:45:19.491 WARN  gatk -   VCF Elapsed Time: 3.377802166s
13:45:19.492 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator2044347494396466169.vcf
13:45:19.495 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
13:45:19.565 INFO  Funcotator - ------------------------------------------------------------
13:45:19.565 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:19.565 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:19.566 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:19.566 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:19.566 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:19 PM UTC
13:45:19.566 INFO  Funcotator - ------------------------------------------------------------
13:45:19.566 INFO  Funcotator - ------------------------------------------------------------
13:45:19.566 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:19.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:19.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:19.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:19.566 INFO  Funcotator - Deflater: IntelDeflater
13:45:19.566 INFO  Funcotator - Inflater: IntelInflater
13:45:19.566 INFO  Funcotator - GCS max retries/reopens: 20
13:45:19.566 INFO  Funcotator - Requester pays: disabled
13:45:19.566 INFO  Funcotator - Initializing engine
13:45:19.568 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
13:45:19.569 INFO  Funcotator - Done initializing engine
13:45:19.569 INFO  Funcotator - Validating sequence dictionaries...
13:45:19.569 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:19.569 INFO  Funcotator - Initializing data sources...
13:45:19.569 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:19.569 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:19.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:19.570 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
13:45:19.570 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
13:45:19.570 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
13:45:19.570 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
13:45:19.571 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
13:45:19.571 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
13:45:19.571 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
13:45:19.571 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
13:45:19.571 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
13:45:19.572 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
13:45:19.572 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:19.572 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
13:45:19.572 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
13:45:19.572 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:19.572 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:19.572 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
13:45:19.573 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
13:45:19.614 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
13:45:19.633 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
13:45:19.639 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
13:45:19.640 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
13:45:19.640 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
13:45:19.640 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
13:45:20.227 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
13:45:20.265 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
13:45:20.265 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:20.266 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
13:45:20.266 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
13:45:20.350 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:20.350 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:20.351 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
13:45:20.377 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:20.378 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:20.378 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
13:45:20.378 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
13:45:20.379 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:20.379 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:20.380 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
13:45:20.382 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
13:45:20.384 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
13:45:20.387 INFO  Funcotator - Initializing Funcotator Engine...
13:45:20.387 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:20.387 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.
13:45:20.387 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator5140777642578581293.maf
13:45:20.388 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
13:45:20.389 INFO  ProgressMeter - Starting traversal
13:45:20.389 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:22.583 INFO  ProgressMeter -             unmapped              0.0                   198           5414.8
13:45:22.583 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:45:22.583 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:45:22.584 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:22 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3087007744
13:45:22.584 WARN  gatk -   MAF Elapsed Time: 3.08502447s
13:45:22.655 INFO  Funcotator - ------------------------------------------------------------
13:45:22.655 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:22.655 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:22.655 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:22.655 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:22.655 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:22 PM UTC
13:45:22.655 INFO  Funcotator - ------------------------------------------------------------
13:45:22.655 INFO  Funcotator - ------------------------------------------------------------
13:45:22.655 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:22.655 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:22.655 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:22.655 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:22.655 INFO  Funcotator - Deflater: IntelDeflater
13:45:22.655 INFO  Funcotator - Inflater: IntelInflater
13:45:22.655 INFO  Funcotator - GCS max retries/reopens: 20
13:45:22.655 INFO  Funcotator - Requester pays: disabled
13:45:22.655 INFO  Funcotator - Initializing engine
13:45:22.658 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
13:45:22.659 INFO  Funcotator - Done initializing engine
13:45:22.659 INFO  Funcotator - Validating sequence dictionaries...
13:45:22.659 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:22.659 INFO  Funcotator - Initializing data sources...
13:45:22.659 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:22.659 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:22.660 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
13:45:22.660 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
13:45:22.660 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
13:45:22.660 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
13:45:22.660 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
13:45:22.661 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
13:45:22.661 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
13:45:22.661 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
13:45:22.661 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
13:45:22.661 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
13:45:22.661 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
13:45:22.661 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:22.662 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
13:45:22.662 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
13:45:22.662 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:22.662 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:22.662 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
13:45:22.663 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
13:45:22.706 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
13:45:22.724 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
13:45:22.731 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
13:45:22.731 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
13:45:22.731 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
13:45:22.732 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
13:45:23.314 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
13:45:23.351 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
13:45:23.351 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:23.352 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
13:45:23.353 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
13:45:23.483 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:23.483 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
13:45:23.484 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
13:45:23.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:23.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:23	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:23.511 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
13:45:23.512 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
13:45:23.512 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:23.512 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:23.513 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
13:45:23.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:23.520 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
13:45:23.523 INFO  Funcotator - Initializing Funcotator Engine...
13:45:23.524 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:23.524 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.
13:45:23.524 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator3750938961221598079.vcf
13:45:23.526 INFO  ProgressMeter - Starting traversal
13:45:23.526 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:24.563 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
13:45:24.564 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
13:45:25.384 INFO  ProgressMeter -             unmapped              0.0                   168           5425.2
13:45:25.384 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
13:45:25.384 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
13:45:25.413 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:25 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3087007744
13:45:25.413 WARN  gatk -   VCF Elapsed Time: 2.826641047s
13:45:25.414 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator3750938961221598079.vcf
13:45:25.417 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
13:45:25.488 INFO  Funcotator - ------------------------------------------------------------
13:45:25.488 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:25.488 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:25.488 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:25.488 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:25.488 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:25 PM UTC
13:45:25.488 INFO  Funcotator - ------------------------------------------------------------
13:45:25.488 INFO  Funcotator - ------------------------------------------------------------
13:45:25.488 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:25.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:25.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:25.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:25.488 INFO  Funcotator - Deflater: IntelDeflater
13:45:25.488 INFO  Funcotator - Inflater: IntelInflater
13:45:25.488 INFO  Funcotator - GCS max retries/reopens: 20
13:45:25.488 INFO  Funcotator - Requester pays: disabled
13:45:25.488 INFO  Funcotator - Initializing engine
13:45:25.490 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
13:45:25.491 INFO  Funcotator - Done initializing engine
13:45:25.491 INFO  Funcotator - Validating sequence dictionaries...
13:45:25.491 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:25.491 INFO  Funcotator - Initializing data sources...
13:45:25.491 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:25.491 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:25.492 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
13:45:25.492 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
13:45:25.492 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
13:45:25.492 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
13:45:25.492 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
13:45:25.493 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
13:45:25.493 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
13:45:25.493 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
13:45:25.493 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
13:45:25.493 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
13:45:25.493 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
13:45:25.493 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:25.494 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
13:45:25.494 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
13:45:25.494 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:25.494 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:25.494 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
13:45:25.494 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
13:45:25.536 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
13:45:25.554 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
13:45:25.561 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
13:45:25.561 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
13:45:25.562 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
13:45:25.562 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
13:45:26.157 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
13:45:26.195 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
13:45:26.195 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:26.196 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
13:45:26.196 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
13:45:26.282 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:26.282 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:26.282 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
13:45:26.309 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:26.309 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:26	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:26.310 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
13:45:26.310 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
13:45:26.311 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:26.311 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:26.311 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
13:45:26.314 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:26.317 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
13:45:26.319 INFO  Funcotator - Initializing Funcotator Engine...
13:45:26.319 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:26.319 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.
13:45:26.319 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator8763243095788518425.maf
13:45:26.319 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
13:45:26.321 INFO  ProgressMeter - Starting traversal
13:45:26.321 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:27.370 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
13:45:27.371 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
13:45:28.169 INFO  ProgressMeter -             unmapped              0.0                   168           5454.5
13:45:28.169 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
13:45:28.169 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
13:45:28.169 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3087007744
13:45:28.170 WARN  gatk -   MAF Elapsed Time: 2.748770722s
13:45:28.236 INFO  Funcotator - ------------------------------------------------------------
13:45:28.236 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:28.236 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:28.236 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:28.236 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:28.236 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:28 PM UTC
13:45:28.236 INFO  Funcotator - ------------------------------------------------------------
13:45:28.236 INFO  Funcotator - ------------------------------------------------------------
13:45:28.236 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:28.236 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:28.236 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:28.236 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:28.236 INFO  Funcotator - Deflater: IntelDeflater
13:45:28.236 INFO  Funcotator - Inflater: IntelInflater
13:45:28.236 INFO  Funcotator - GCS max retries/reopens: 20
13:45:28.236 INFO  Funcotator - Requester pays: disabled
13:45:28.236 INFO  Funcotator - Initializing engine
13:45:28.239 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
13:45:28.240 INFO  Funcotator - Done initializing engine
13:45:28.240 INFO  Funcotator - Validating sequence dictionaries...
13:45:28.240 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:28.240 INFO  Funcotator - Initializing data sources...
13:45:28.240 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:28.240 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:28.240 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
13:45:28.240 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
13:45:28.241 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
13:45:28.241 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
13:45:28.241 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
13:45:28.241 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
13:45:28.241 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
13:45:28.241 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
13:45:28.242 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
13:45:28.242 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
13:45:28.242 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
13:45:28.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:28.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:28.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:28.243 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:28.243 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:28.243 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
13:45:28.243 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
13:45:28.284 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:28.302 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
13:45:28.308 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
13:45:28.309 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
13:45:28.309 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
13:45:28.309 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
13:45:28.846 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
13:45:28.885 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
13:45:28.885 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:28.885 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
13:45:28.886 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
13:45:28.970 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:28.970 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:28.971 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
13:45:29.061 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
13:45:29.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:29.062 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
13:45:29.062 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
13:45:29.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:29.063 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:29.064 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
13:45:29.066 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:29.068 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
13:45:29.070 INFO  Funcotator - Initializing Funcotator Engine...
13:45:29.070 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:29.070 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.
13:45:29.070 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator13539204056804197375.vcf
13:45:29.072 INFO  ProgressMeter - Starting traversal
13:45:29.072 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:29.082 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
13:45:29.082 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:45:29.082 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:29.083 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3087007744
13:45:29.083 WARN  gatk -   VCF Elapsed Time: 0.91115226s
13:45:29.084 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator13539204056804197375.vcf
13:45:29.085 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
13:45:29.151 INFO  Funcotator - ------------------------------------------------------------
13:45:29.151 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:29.151 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:29.151 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:29.151 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:29.151 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:29 PM UTC
13:45:29.151 INFO  Funcotator - ------------------------------------------------------------
13:45:29.151 INFO  Funcotator - ------------------------------------------------------------
13:45:29.151 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:29.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:29.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:29.151 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:29.151 INFO  Funcotator - Deflater: IntelDeflater
13:45:29.151 INFO  Funcotator - Inflater: IntelInflater
13:45:29.151 INFO  Funcotator - GCS max retries/reopens: 20
13:45:29.151 INFO  Funcotator - Requester pays: disabled
13:45:29.151 INFO  Funcotator - Initializing engine
13:45:29.153 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
13:45:29.154 INFO  Funcotator - Done initializing engine
13:45:29.154 INFO  Funcotator - Validating sequence dictionaries...
13:45:29.154 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:29.154 INFO  Funcotator - Initializing data sources...
13:45:29.154 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:29.154 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:29.154 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
13:45:29.155 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
13:45:29.155 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
13:45:29.155 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
13:45:29.155 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
13:45:29.155 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
13:45:29.155 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
13:45:29.156 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
13:45:29.156 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
13:45:29.156 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
13:45:29.156 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
13:45:29.156 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/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:29.156 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
13:45:29.157 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
13:45:29.157 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:29.157 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:29.157 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
13:45:29.157 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
13:45:29.198 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
13:45:29.217 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
13:45:29.224 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
13:45:29.224 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
13:45:29.224 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
13:45:29.225 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
13:45:29.762 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
13:45:29.799 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
13:45:29.799 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:29.800 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
13:45:29.800 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
13:45:29.936 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:29.936 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:29.937 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
13:45:29.964 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:29.964 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:29.964 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
13:45:29.965 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
13:45:29.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:29.965 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:29.966 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
13:45:29.968 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:29.970 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
13:45:29.972 INFO  Funcotator - Initializing Funcotator Engine...
13:45:29.973 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:29.973 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.
13:45:29.973 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator16170819141467036465.maf
13:45:29.973 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
13:45:29.973 INFO  ProgressMeter - Starting traversal
13:45:29.973 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:29.984 INFO  ProgressMeter -             unmapped              0.0                     1           5454.5
13:45:29.984 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:45:29.984 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:29.984 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:29 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3087007744
13:45:29.984 WARN  gatk -   MAF Elapsed Time: 0.898260838s
13:45:30.052 INFO  Funcotator - ------------------------------------------------------------
13:45:30.052 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:30.052 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:30.052 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:30.052 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:30.053 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:30 PM UTC
13:45:30.053 INFO  Funcotator - ------------------------------------------------------------
13:45:30.053 INFO  Funcotator - ------------------------------------------------------------
13:45:30.053 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:30.053 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:30.053 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:30.053 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:30.053 INFO  Funcotator - Deflater: IntelDeflater
13:45:30.053 INFO  Funcotator - Inflater: IntelInflater
13:45:30.053 INFO  Funcotator - GCS max retries/reopens: 20
13:45:30.053 INFO  Funcotator - Requester pays: disabled
13:45:30.053 INFO  Funcotator - Initializing engine
13:45:30.084 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
13:45:30.106 INFO  Funcotator - Done initializing engine
13:45:30.106 INFO  Funcotator - Validating sequence dictionaries...
13:45:30.113 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:30.114 INFO  Funcotator - Initializing data sources...
13:45:30.114 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:30.114 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:30.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
13:45:30.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
13:45:30.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
13:45:30.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
13:45:30.115 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
13:45:30.115 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
13:45:30.115 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
13:45:30.115 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
13:45:30.115 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
13:45:30.115 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
13:45:30.116 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
13:45:30.116 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
13:45:30.116 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
13:45:30.116 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:30.116 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
13:45:30.158 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
13:45:30.176 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
13:45:30.183 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
13:45:30.183 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
13:45:30.183 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
13:45:30.184 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
13:45:30.707 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
13:45:30.821 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
13:45:30.821 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:30.822 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
13:45:30.822 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
13:45:30.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
13:45:30.823 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
13:45:30.824 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
13:45:30.824 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:30.824 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
13:45:30.826 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
13:45:30.827 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
13:45:30.829 INFO  Funcotator - Initializing Funcotator Engine...
13:45:30.832 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:30.832 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator11580703764055540729.vcf
13:45:30.843 INFO  ProgressMeter - Starting traversal
13:45:30.844 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:30.869 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.
13:45:30.871 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
13:45:30.874 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:30.877 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:30.877 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:30.878 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:30.878 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:30.878 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:30.879 INFO  ProgressMeter -             unmapped              0.0                     5           8571.4
13:45:30.879 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
13:45:30.879 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:30.887 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:30 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3087007744
13:45:30.887 WARN  gatk -   VCF Elapsed Time: 0.90249564s
13:45:30.888 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator11580703764055540729.vcf
13:45:30.899 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
13:45:30.974 INFO  Funcotator - ------------------------------------------------------------
13:45:30.974 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:30.974 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:30.974 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:30.974 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:30.974 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:30 PM UTC
13:45:30.974 INFO  Funcotator - ------------------------------------------------------------
13:45:30.974 INFO  Funcotator - ------------------------------------------------------------
13:45:30.974 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:30.974 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:30.974 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:30.974 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:30.974 INFO  Funcotator - Deflater: IntelDeflater
13:45:30.974 INFO  Funcotator - Inflater: IntelInflater
13:45:30.974 INFO  Funcotator - GCS max retries/reopens: 20
13:45:30.974 INFO  Funcotator - Requester pays: disabled
13:45:30.975 INFO  Funcotator - Initializing engine
13:45:31.000 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
13:45:31.021 INFO  Funcotator - Done initializing engine
13:45:31.022 INFO  Funcotator - Validating sequence dictionaries...
13:45:31.028 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:31.029 INFO  Funcotator - Initializing data sources...
13:45:31.029 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:31.029 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:31.029 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
13:45:31.029 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
13:45:31.029 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
13:45:31.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
13:45:31.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
13:45:31.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
13:45:31.030 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
13:45:31.030 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
13:45:31.030 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
13:45:31.030 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
13:45:31.031 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
13:45:31.031 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
13:45:31.031 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
13:45:31.031 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:31.031 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
13:45:31.073 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/hg38/simple_uniprot_Dec012014.tsv
13:45:31.091 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
13:45:31.098 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
13:45:31.098 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
13:45:31.098 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
13:45:31.099 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
13:45:31.670 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
13:45:31.733 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
13:45:31.733 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:31.734 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
13:45:31.735 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
13:45:31.736 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/hg38/achilles_lineage_results.import.txt
13:45:31.736 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/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:31.736 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
13:45:31.737 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:31.737 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
13:45:31.738 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
13:45:31.740 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
13:45:31.742 INFO  Funcotator - Initializing Funcotator Engine...
13:45:31.745 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:31.745 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator15339532974082417004.maf
13:45:31.747 INFO  ProgressMeter - Starting traversal
13:45:31.747 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:31.772 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.
13:45:31.772 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
13:45:31.774 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:31.777 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:31.777 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
13:45:31.777 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:31.777 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:31.777 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
13:45:31.778 INFO  ProgressMeter -             unmapped              0.0                     5           9677.4
13:45:31.778 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
13:45:31.778 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:31.779 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:31 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3087007744
13:45:31.779 WARN  gatk -   MAF Elapsed Time: 0.871891694s
13:45:31.846 INFO  Funcotator - ------------------------------------------------------------
13:45:31.847 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:31.847 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:31.847 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:31.847 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:31.847 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:31 PM UTC
13:45:31.847 INFO  Funcotator - ------------------------------------------------------------
13:45:31.847 INFO  Funcotator - ------------------------------------------------------------
13:45:31.847 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:31.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:31.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:31.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:31.847 INFO  Funcotator - Deflater: IntelDeflater
13:45:31.847 INFO  Funcotator - Inflater: IntelInflater
13:45:31.847 INFO  Funcotator - GCS max retries/reopens: 20
13:45:31.847 INFO  Funcotator - Requester pays: disabled
13:45:31.847 INFO  Funcotator - Initializing engine
13:45:31.849 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
13:45:31.851 INFO  Funcotator - Done initializing engine
13:45:31.851 INFO  Funcotator - Validating sequence dictionaries...
13:45:31.851 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:31.851 INFO  Funcotator - Initializing data sources...
13:45:31.851 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:31.851 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:31.851 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
13:45:31.851 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
13:45:31.852 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
13:45:31.852 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
13:45:31.852 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
13:45:31.852 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
13:45:31.852 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
13:45:31.852 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
13:45:31.853 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
13:45:31.853 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
13:45:31.853 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
13:45:31.853 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:31.853 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
13:45:31.853 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
13:45:31.853 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:31.853 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:31.853 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
13:45:31.854 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
13:45:31.895 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
13:45:31.913 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
13:45:31.920 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
13:45:31.920 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
13:45:31.920 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
13:45:31.921 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
13:45:32.501 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:32.537 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
13:45:32.538 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:32.538 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
13:45:32.539 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
13:45:32.622 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:32.623 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:32.623 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
13:45:32.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:32.650 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:32	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:32.651 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
13:45:32.651 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
13:45:32.651 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:32.651 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:32.652 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
13:45:32.654 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
13:45:32.657 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
13:45:32.659 INFO  Funcotator - Initializing Funcotator Engine...
13:45:32.659 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:32.659 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.
13:45:32.659 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator8042527120686014410.vcf
13:45:32.663 INFO  ProgressMeter - Starting traversal
13:45:32.663 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:38.319 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
13:45:38.320 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
13:45:38.321 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          15980.9
13:45:38.321 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
13:45:38.321 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
13:45:38.344 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:38 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3112173568
13:45:38.344 WARN  gatk -   VCF Elapsed Time: 6.563323391s
13:45:38.345 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator8042527120686014410.vcf
13:45:38.353 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
13:45:38.439 INFO  Funcotator - ------------------------------------------------------------
13:45:38.439 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:38.439 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:38.439 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:38.439 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:38.439 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:38 PM UTC
13:45:38.439 INFO  Funcotator - ------------------------------------------------------------
13:45:38.439 INFO  Funcotator - ------------------------------------------------------------
13:45:38.439 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:38.439 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:38.439 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:38.440 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:38.440 INFO  Funcotator - Deflater: IntelDeflater
13:45:38.440 INFO  Funcotator - Inflater: IntelInflater
13:45:38.440 INFO  Funcotator - GCS max retries/reopens: 20
13:45:38.440 INFO  Funcotator - Requester pays: disabled
13:45:38.440 INFO  Funcotator - Initializing engine
13:45:38.442 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
13:45:38.443 INFO  Funcotator - Done initializing engine
13:45:38.443 INFO  Funcotator - Validating sequence dictionaries...
13:45:38.443 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:38.443 INFO  Funcotator - Initializing data sources...
13:45:38.443 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:38.443 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:38.444 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
13:45:38.444 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
13:45:38.444 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
13:45:38.444 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
13:45:38.444 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
13:45:38.444 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
13:45:38.444 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
13:45:38.445 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
13:45:38.445 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:38.445 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
13:45:38.445 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
13:45:38.445 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:38.445 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
13:45:38.445 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
13:45:38.446 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:38.446 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:38.446 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
13:45:38.446 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
13:45:38.489 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
13:45:38.506 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
13:45:38.513 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
13:45:38.513 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
13:45:38.513 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
13:45:38.514 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
13:45:39.048 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
13:45:39.088 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
13:45:39.088 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:39.088 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
13:45:39.089 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
13:45:39.258 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:39.258 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:39.259 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
13:45:39.286 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:39.286 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:45:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:39.286 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:39.287 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
13:45:39.287 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:39.287 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:39.288 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
13:45:39.290 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:39.292 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
13:45:39.294 INFO  Funcotator - Initializing Funcotator Engine...
13:45:39.294 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:39.294 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.
13:45:39.294 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator14183509395977496405.maf
13:45:39.294 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
13:45:39.295 INFO  ProgressMeter - Starting traversal
13:45:39.295 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:44.498 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
13:45:44.498 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
13:45:44.499 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17375.1
13:45:44.499 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
13:45:44.499 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
13:45:44.500 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3112173568
13:45:44.500 WARN  gatk -   MAF Elapsed Time: 6.12755094s
13:45:44.580 INFO  Funcotator - ------------------------------------------------------------
13:45:44.580 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:44.580 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:44.580 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:44.580 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:44.580 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:44 PM UTC
13:45:44.580 INFO  Funcotator - ------------------------------------------------------------
13:45:44.580 INFO  Funcotator - ------------------------------------------------------------
13:45:44.580 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:44.580 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:44.580 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:44.580 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:44.580 INFO  Funcotator - Deflater: IntelDeflater
13:45:44.580 INFO  Funcotator - Inflater: IntelInflater
13:45:44.580 INFO  Funcotator - GCS max retries/reopens: 20
13:45:44.580 INFO  Funcotator - Requester pays: disabled
13:45:44.580 INFO  Funcotator - Initializing engine
13:45:44.582 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
13:45:44.584 INFO  Funcotator - Done initializing engine
13:45:44.584 INFO  Funcotator - Validating sequence dictionaries...
13:45:44.584 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:44.584 INFO  Funcotator - Initializing data sources...
13:45:44.584 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:44.584 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:44.584 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
13:45:44.584 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
13:45:44.585 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
13:45:44.585 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
13:45:44.585 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
13:45:44.585 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
13:45:44.585 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
13:45:44.585 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
13:45:44.585 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
13:45:44.586 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
13:45:44.586 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
13:45:44.586 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:44.586 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
13:45:44.586 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
13:45:44.586 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
13:45:44.586 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:44.586 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
13:45:44.587 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
13:45:44.630 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
13:45:44.647 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
13:45:44.654 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
13:45:44.654 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
13:45:44.655 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
13:45:44.655 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
13:45:45.193 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:45.291 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
13:45:45.291 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:45.292 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
13:45:45.292 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
13:45:45.376 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:45.377 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:45.377 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
13:45:45.404 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:45.404 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:45.405 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
13:45:45.405 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
13:45:45.405 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:45.405 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:45.406 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
13:45:45.408 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
13:45:45.411 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
13:45:45.413 INFO  Funcotator - Initializing Funcotator Engine...
13:45:45.413 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:45.413 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.
13:45:45.413 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator15964849343808609934.vcf
13:45:45.414 INFO  ProgressMeter - Starting traversal
13:45:45.414 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:47.418 INFO  ProgressMeter -             unmapped              0.0                   198           5928.1
13:45:47.418 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:45:47.418 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:45:47.427 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3112173568
13:45:47.495 INFO  Funcotator - ------------------------------------------------------------
13:45:47.495 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:47.495 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:47.496 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:47.496 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:47.496 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:47 PM UTC
13:45:47.496 INFO  Funcotator - ------------------------------------------------------------
13:45:47.496 INFO  Funcotator - ------------------------------------------------------------
13:45:47.496 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:47.496 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:47.496 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:47.496 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:47.496 INFO  Funcotator - Deflater: IntelDeflater
13:45:47.496 INFO  Funcotator - Inflater: IntelInflater
13:45:47.496 INFO  Funcotator - GCS max retries/reopens: 20
13:45:47.496 INFO  Funcotator - Requester pays: disabled
13:45:47.496 INFO  Funcotator - Initializing engine
13:45:47.498 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
13:45:47.499 INFO  Funcotator - Done initializing engine
13:45:47.499 INFO  Funcotator - Validating sequence dictionaries...
13:45:47.499 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:47.499 INFO  Funcotator - Initializing data sources...
13:45:47.499 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:47.499 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:47.500 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
13:45:47.500 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
13:45:47.500 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
13:45:47.500 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
13:45:47.500 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
13:45:47.501 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
13:45:47.501 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
13:45:47.501 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
13:45:47.501 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:47.501 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
13:45:47.501 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
13:45:47.502 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:47.502 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
13:45:47.502 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
13:45:47.502 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:47.502 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:47.502 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
13:45:47.503 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
13:45:47.545 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
13:45:47.563 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
13:45:47.570 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
13:45:47.570 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
13:45:47.570 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
13:45:47.571 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
13:45:48.181 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
13:45:48.218 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
13:45:48.218 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:48.219 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
13:45:48.219 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
13:45:48.303 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:48.304 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:48.304 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
13:45:48.332 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:48.332 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:48.332 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
13:45:48.333 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
13:45:48.334 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:48.334 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:48.335 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
13:45:48.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:48.339 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
13:45:48.341 INFO  Funcotator - Initializing Funcotator Engine...
13:45:48.341 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:48.341 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
13:45:48.341 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator13816815650697764436.maf
13:45:48.341 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
13:45:48.342 INFO  ProgressMeter - Starting traversal
13:45:48.342 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:50.346 INFO  ProgressMeter -             unmapped              0.0                   198           5928.1
13:45:50.346 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:45:50.346 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:45:50.346 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3112173568
13:45:50.415 INFO  Funcotator - ------------------------------------------------------------
13:45:50.415 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:50.415 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:50.415 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:50.415 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:50.415 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:50 PM UTC
13:45:50.415 INFO  Funcotator - ------------------------------------------------------------
13:45:50.415 INFO  Funcotator - ------------------------------------------------------------
13:45:50.415 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:50.415 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:50.415 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:50.416 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:50.416 INFO  Funcotator - Deflater: IntelDeflater
13:45:50.416 INFO  Funcotator - Inflater: IntelInflater
13:45:50.416 INFO  Funcotator - GCS max retries/reopens: 20
13:45:50.416 INFO  Funcotator - Requester pays: disabled
13:45:50.416 INFO  Funcotator - Initializing engine
13:45:50.418 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
13:45:50.419 INFO  Funcotator - Done initializing engine
13:45:50.419 INFO  Funcotator - Validating sequence dictionaries...
13:45:50.419 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:50.419 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3112173568
13:45:50.488 INFO  Funcotator - ------------------------------------------------------------
13:45:50.488 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:50.488 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:50.488 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:50.488 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:50.488 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:50 PM UTC
13:45:50.488 INFO  Funcotator - ------------------------------------------------------------
13:45:50.488 INFO  Funcotator - ------------------------------------------------------------
13:45:50.488 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:50.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:50.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:50.488 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:50.488 INFO  Funcotator - Deflater: IntelDeflater
13:45:50.488 INFO  Funcotator - Inflater: IntelInflater
13:45:50.488 INFO  Funcotator - GCS max retries/reopens: 20
13:45:50.488 INFO  Funcotator - Requester pays: disabled
13:45:50.488 INFO  Funcotator - Initializing engine
13:45:50.489 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
13:45:50.508 INFO  Funcotator - Done initializing engine
13:45:50.508 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:50.508 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:50.508 INFO  Funcotator - Initializing data sources...
13:45:50.508 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:45:50.508 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:50.508 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
13:45:50.508 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
13:45:50.508 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
13:45:50.508 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:50.508 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
13:45:50.508 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:50.509 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
13:45:50.509 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
13:45:50.510 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
13:45:50.510 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:45:50.510 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
13:45:50.519 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
13:45:50.528 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
13:45:50.537 INFO  Funcotator - Initializing Funcotator Engine...
13:45:50.541 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:50.541 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14747234033916131127.vcf
13:45:50.554 INFO  ProgressMeter - Starting traversal
13:45:50.554 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:50.585 INFO  ProgressMeter -             unmapped              0.0                   100         193548.4
13:45:50.585 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
13:45:50.585 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:45:50.591 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3112173568
13:45:50.591 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14747234033916131127.vcf
13:45:50.670 INFO  Funcotator - ------------------------------------------------------------
13:45:50.670 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:50.670 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:50.670 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:50.670 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:50.670 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:50 PM UTC
13:45:50.670 INFO  Funcotator - ------------------------------------------------------------
13:45:50.670 INFO  Funcotator - ------------------------------------------------------------
13:45:50.670 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:50.670 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:50.670 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:50.670 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:50.670 INFO  Funcotator - Deflater: IntelDeflater
13:45:50.671 INFO  Funcotator - Inflater: IntelInflater
13:45:50.671 INFO  Funcotator - GCS max retries/reopens: 20
13:45:50.671 INFO  Funcotator - Requester pays: disabled
13:45:50.671 INFO  Funcotator - Initializing engine
13:45:50.672 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
13:45:50.674 INFO  Funcotator - Done initializing engine
13:45:50.675 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:50.675 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:50.675 INFO  Funcotator - Initializing data sources...
13:45:50.675 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:45:50.675 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:50.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
13:45:50.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
13:45:50.675 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
13:45:50.675 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:50.675 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
13:45:50.675 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:50.676 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
13:45:50.676 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
13:45:50.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:45:50.677 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:45:50.677 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:45:50.678 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:45:50.680 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
13:45:50.681 INFO  Funcotator - Initializing Funcotator Engine...
13:45:50.681 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:45:50.681 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.
13:45:50.681 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13120154785118882573.vcf
13:45:50.687 INFO  ProgressMeter - Starting traversal
13:45:50.687 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:50.696 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
13:45:50.696 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
13:45:50.696 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:45:50.699 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3112173568
13:45:50.699 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13120154785118882573.vcf
13:45:50.774 INFO  Funcotator - ------------------------------------------------------------
13:45:50.774 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:50.774 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:50.774 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:50.774 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:50.774 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:50 PM UTC
13:45:50.774 INFO  Funcotator - ------------------------------------------------------------
13:45:50.774 INFO  Funcotator - ------------------------------------------------------------
13:45:50.774 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:50.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:50.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:50.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:50.774 INFO  Funcotator - Deflater: IntelDeflater
13:45:50.774 INFO  Funcotator - Inflater: IntelInflater
13:45:50.774 INFO  Funcotator - GCS max retries/reopens: 20
13:45:50.774 INFO  Funcotator - Requester pays: disabled
13:45:50.774 INFO  Funcotator - Initializing engine
13:45:50.775 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
13:45:50.798 INFO  Funcotator - Done initializing engine
13:45:50.798 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:50.798 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:50.798 INFO  Funcotator - Initializing data sources...
13:45:50.798 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:45:50.798 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:50.799 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
13:45:50.799 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
13:45:50.799 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
13:45:50.799 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:50.799 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
13:45:50.799 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:50.800 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
13:45:50.800 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
13:45:50.801 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
13:45:50.801 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:45:50.801 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/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:45:50.815 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
13:45:50.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:45:50.839 INFO  Funcotator - Initializing Funcotator Engine...
13:45:50.843 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:50.843 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3562474250409385479.vcf
13:45:50.854 INFO  ProgressMeter - Starting traversal
13:45:50.854 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:50.859 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)
13:45:50.859 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)
13:45:50.859 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.859 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:45:50.860 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
13:45:50.860 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
13:45:50.862 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.862 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:45:50.862 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
13:45:50.862 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
13:45:50.863 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)
13:45:50.863 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)
13:45:50.863 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.863 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:45:50.863 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
13:45:50.863 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
13:45:50.864 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)
13:45:50.864 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)
13:45:50.864 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
13:45:50.864 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
13:45:50.864 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
13:45:50.864 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
13:45:50.865 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.865 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:45:50.865 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
13:45:50.865 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
13:45:50.866 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.866 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:45:50.866 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
13:45:50.866 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
13:45:50.867 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)
13:45:50.867 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)
13:45:50.867 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
13:45:50.867 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:45:50.867 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
13:45:50.867 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
13:45:50.868 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)
13:45:50.868 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)
13:45:50.868 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.868 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:45:50.868 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
13:45:50.868 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
13:45:50.869 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
13:45:50.869 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:45:50.869 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
13:45:50.869 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
13:45:50.870 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)
13:45:50.870 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)
13:45:50.870 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:45:50.870 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:45:50.871 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
13:45:50.871 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
13:45:50.871 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
13:45:50.871 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
13:45:50.871 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:45:50.876 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3112173568
13:45:50.877 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3562474250409385479.vcf
13:45:50.954 INFO  Funcotator - ------------------------------------------------------------
13:45:50.954 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:50.954 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:50.954 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:50.954 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:50.954 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:50 PM UTC
13:45:50.954 INFO  Funcotator - ------------------------------------------------------------
13:45:50.954 INFO  Funcotator - ------------------------------------------------------------
13:45:50.954 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:50.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:50.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:50.954 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:50.954 INFO  Funcotator - Deflater: IntelDeflater
13:45:50.954 INFO  Funcotator - Inflater: IntelInflater
13:45:50.954 INFO  Funcotator - GCS max retries/reopens: 20
13:45:50.954 INFO  Funcotator - Requester pays: disabled
13:45:50.954 INFO  Funcotator - Initializing engine
13:45:50.957 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
13:45:50.958 INFO  Funcotator - Done initializing engine
13:45:50.958 INFO  Funcotator - Validating sequence dictionaries...
13:45:50.958 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:50.958 INFO  Funcotator - Initializing data sources...
13:45:50.958 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:50.958 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:50.959 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
13:45:50.959 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
13:45:50.959 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
13:45:50.959 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
13:45:50.959 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
13:45:50.960 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
13:45:50.960 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
13:45:50.960 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
13:45:50.960 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
13:45:50.960 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
13:45:50.960 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
13:45:50.960 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:50.961 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
13:45:50.961 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
13:45:50.961 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:50.961 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:50.961 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
13:45:50.961 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
13:45:51.003 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:51.021 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
13:45:51.028 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
13:45:51.028 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
13:45:51.028 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
13:45:51.029 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
13:45:51.604 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
13:45:51.681 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
13:45:51.681 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:51.682 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
13:45:51.682 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
13:45:51.769 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:51.770 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:51.770 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
13:45:51.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:51.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:45:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:51.798 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:51.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:51.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:51.799 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:51.800 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
13:45:51.802 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
13:45:51.805 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
13:45:51.807 INFO  Funcotator - Initializing Funcotator Engine...
13:45:51.807 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:51.807 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.
13:45:51.807 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator15698433037094130079.vcf
13:45:51.811 INFO  ProgressMeter - Starting traversal
13:45:51.811 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:51.860 INFO  ProgressMeter -             unmapped              0.0                     1           1224.5
13:45:51.860 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:45:51.860 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:51.861 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:51 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3112173568
13:45:51.861 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator15698433037094130079.vcf
13:45:51.932 INFO  Funcotator - ------------------------------------------------------------
13:45:51.932 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:51.932 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:51.932 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:51.932 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:51.932 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:51 PM UTC
13:45:51.932 INFO  Funcotator - ------------------------------------------------------------
13:45:51.932 INFO  Funcotator - ------------------------------------------------------------
13:45:51.933 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:51.933 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:51.933 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:51.933 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:51.933 INFO  Funcotator - Deflater: IntelDeflater
13:45:51.933 INFO  Funcotator - Inflater: IntelInflater
13:45:51.933 INFO  Funcotator - GCS max retries/reopens: 20
13:45:51.933 INFO  Funcotator - Requester pays: disabled
13:45:51.933 INFO  Funcotator - Initializing engine
13:45:51.935 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
13:45:51.936 INFO  Funcotator - Done initializing engine
13:45:51.936 INFO  Funcotator - Validating sequence dictionaries...
13:45:51.936 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:51.936 INFO  Funcotator - Initializing data sources...
13:45:51.937 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:51.937 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:51.937 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
13:45:51.937 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
13:45:51.937 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
13:45:51.937 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
13:45:51.938 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
13:45:51.938 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
13:45:51.938 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
13:45:51.938 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
13:45:51.938 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
13:45:51.938 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
13:45:51.938 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
13:45:51.939 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:51.939 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
13:45:51.939 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
13:45:51.939 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:51.939 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:51.939 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
13:45:51.940 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
13:45:51.983 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:52.001 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
13:45:52.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:45:52.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:45:52.008 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:45:52.008 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
13:45:52.687 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
13:45:52.724 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
13:45:52.724 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:52.725 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
13:45:52.725 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
13:45:52.810 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:52.810 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:52.811 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
13:45:52.838 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
13:45:52.838 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
WARNING	2025-05-27 13:45:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:52.838 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
13:45:52.839 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
13:45:52.839 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
13:45:52.839 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:52.840 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
13:45:52.842 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:52.844 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
13:45:52.846 INFO  Funcotator - Initializing Funcotator Engine...
13:45:52.846 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:45:52.847 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.
13:45:52.847 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator426821847359146288.vcf
13:45:52.850 INFO  ProgressMeter - Starting traversal
13:45:52.850 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:52.857 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.895 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
13:45:52.899 INFO  ProgressMeter -             unmapped              0.0                     2           2449.0
13:45:52.899 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:45:52.899 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:52.899 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:52 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3135242240
13:45:52.900 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator426821847359146288.vcf
13:45:52.969 INFO  Funcotator - ------------------------------------------------------------
13:45:52.969 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:52.969 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:52.969 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:52.969 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:52.969 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:52 PM UTC
13:45:52.969 INFO  Funcotator - ------------------------------------------------------------
13:45:52.969 INFO  Funcotator - ------------------------------------------------------------
13:45:52.969 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:52.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:52.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:52.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:52.969 INFO  Funcotator - Deflater: IntelDeflater
13:45:52.969 INFO  Funcotator - Inflater: IntelInflater
13:45:52.969 INFO  Funcotator - GCS max retries/reopens: 20
13:45:52.969 INFO  Funcotator - Requester pays: disabled
13:45:52.969 INFO  Funcotator - Initializing engine
13:45:52.971 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
13:45:52.972 INFO  Funcotator - Done initializing engine
13:45:52.972 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:52.972 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:52.972 INFO  Funcotator - Initializing data sources...
13:45:52.972 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:52.972 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:52.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:52.973 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
13:45:52.973 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
13:45:52.973 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
13:45:52.973 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
13:45:52.973 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
13:45:52.973 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
13:45:52.973 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
13:45:52.974 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:52.974 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
13:45:52.974 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
13:45:52.974 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:52.974 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
13:45:52.974 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
13:45:52.975 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:52.975 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:52.975 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
13:45:52.975 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
13:45:53.060 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
13:45:53.079 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
13:45:53.085 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
13:45:53.086 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
13:45:53.086 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
13:45:53.086 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
13:45:53.733 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
13:45:53.772 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
13:45:53.772 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:53.772 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
13:45:53.773 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
13:45:53.872 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:53.872 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:53.873 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
13:45:53.900 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:53.900 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:53.901 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:53.901 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:53.902 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:53.902 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:53.903 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
13:45:53.905 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:53.908 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
13:45:53.910 INFO  Funcotator - Initializing Funcotator Engine...
13:45:53.910 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:45:53.910 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.
13:45:53.910 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
13:45:53.910 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
13:45:53.910 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
13:45:53.910 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16556181013486415269.vcf
13:45:53.914 INFO  ProgressMeter - Starting traversal
13:45:53.914 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:53.947 INFO  ProgressMeter -             unmapped              0.0                     1           1818.2
13:45:53.947 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:45:53.948 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:53.948 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:53 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3242196992
13:45:53.949 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16556181013486415269.vcf
13:45:53.950 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 1:45:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3242196992
[May 27, 2025 at 1:45:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3242196992
13:45:54.200 INFO  Funcotator - ------------------------------------------------------------
13:45:54.200 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:54.200 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:54.200 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:54.200 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:54.200 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:54 PM UTC
13:45:54.200 INFO  Funcotator - ------------------------------------------------------------
13:45:54.200 INFO  Funcotator - ------------------------------------------------------------
13:45:54.200 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:54.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:54.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:54.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:54.200 INFO  Funcotator - Deflater: IntelDeflater
13:45:54.200 INFO  Funcotator - Inflater: IntelInflater
13:45:54.200 INFO  Funcotator - GCS max retries/reopens: 20
13:45:54.200 INFO  Funcotator - Requester pays: disabled
13:45:54.200 INFO  Funcotator - Initializing engine
13:45:54.201 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
13:45:54.216 INFO  Funcotator - Done initializing engine
13:45:54.216 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:54.216 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:54.216 INFO  Funcotator - Initializing data sources...
13:45:54.216 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:45:54.216 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:54.217 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
13:45:54.217 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
13:45:54.217 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
13:45:54.217 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:54.217 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
13:45:54.217 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:54.218 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
13:45:54.218 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
13:45:54.218 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:45:54.218 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:45:54.219 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
13:45:54.227 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
13:45:54.236 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
13:45:54.244 INFO  Funcotator - Initializing Funcotator Engine...
13:45:54.248 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:54.248 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11905051498743116113.vcf
13:45:54.261 INFO  ProgressMeter - Starting traversal
13:45:54.261 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:54.289 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
13:45:54.289 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
13:45:54.289 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:45:54.336 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3242196992
13:45:54.337 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11905051498743116113.vcf
13:45:54.419 INFO  Funcotator - ------------------------------------------------------------
13:45:54.419 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:54.419 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:54.419 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:54.419 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:54.419 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:54 PM UTC
13:45:54.419 INFO  Funcotator - ------------------------------------------------------------
13:45:54.419 INFO  Funcotator - ------------------------------------------------------------
13:45:54.419 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:54.419 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:54.419 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:54.419 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:54.419 INFO  Funcotator - Deflater: IntelDeflater
13:45:54.419 INFO  Funcotator - Inflater: IntelInflater
13:45:54.419 INFO  Funcotator - GCS max retries/reopens: 20
13:45:54.419 INFO  Funcotator - Requester pays: disabled
13:45:54.419 INFO  Funcotator - Initializing engine
13:45:54.421 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
13:45:54.422 INFO  Funcotator - Done initializing engine
13:45:54.422 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:54.422 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:54.422 INFO  Funcotator - Initializing data sources...
13:45:54.422 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/
13:45:54.422 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:54.423 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
13:45:54.423 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
13:45:54.423 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
13:45:54.423 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:54.423 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
13:45:54.423 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:54.423 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
13:45:54.424 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
13:45:54.424 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
13:45:54.424 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
13:45:54.425 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
13:45:54.427 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
13:45:54.429 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
13:45:54.431 INFO  Funcotator - Initializing Funcotator Engine...
13:45:54.431 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:45:54.431 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.
13:45:54.431 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:54.431 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing15047531371162127283.vcf
13:45:54.434 INFO  ProgressMeter - Starting traversal
13:45:54.434 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:54.457 INFO  ProgressMeter -             unmapped              0.0                     1           2608.7
13:45:54.457 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:45:54.457 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
13:45:54.459 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3242196992
13:45:54.460 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing15047531371162127283.vcf
13:45:54.528 INFO  Funcotator - ------------------------------------------------------------
13:45:54.528 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:54.528 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:54.528 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:54.528 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:54.528 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:54 PM UTC
13:45:54.528 INFO  Funcotator - ------------------------------------------------------------
13:45:54.528 INFO  Funcotator - ------------------------------------------------------------
13:45:54.528 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:54.528 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:54.528 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:54.528 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:54.528 INFO  Funcotator - Deflater: IntelDeflater
13:45:54.528 INFO  Funcotator - Inflater: IntelInflater
13:45:54.528 INFO  Funcotator - GCS max retries/reopens: 20
13:45:54.528 INFO  Funcotator - Requester pays: disabled
13:45:54.528 INFO  Funcotator - Initializing engine
13:45:54.529 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
13:45:54.529 INFO  Funcotator - Done initializing engine
13:45:54.529 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:54.529 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:54.529 INFO  Funcotator - Initializing data sources...
13:45:54.529 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:54.529 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:54.530 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
13:45:54.530 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
13:45:54.530 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
13:45:54.530 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
13:45:54.530 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
13:45:54.530 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
13:45:54.531 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
13:45:54.531 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
13:45:54.531 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
13:45:54.531 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
13:45:54.531 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
13:45:54.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:54.532 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
13:45:54.532 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
13:45:54.532 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
13:45:54.532 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:54.532 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
13:45:54.532 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
13:45:54.575 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
13:45:54.593 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
13:45:54.600 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
13:45:54.600 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
13:45:54.600 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:45:54.601 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
13:45:55.300 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
13:45:55.343 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
13:45:55.343 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:55.344 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
13:45:55.345 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
13:45:55.433 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:55.434 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:55.434 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
13:45:55.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:55.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:55	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:55.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:55.464 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:55.464 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:55.464 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:55.465 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
13:45:55.467 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:55.469 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
13:45:55.471 INFO  Funcotator - Initializing Funcotator Engine...
13:45:55.472 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
13:45:55.472 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:55.472 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:55.472 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:55.472 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:55.472 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:55.472 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13664184034267264021.vcf
13:45:55.473 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
13:45:55.474 INFO  ProgressMeter - Starting traversal
13:45:55.474 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:55.493 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
13:45:55.493 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:55.493 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:55.496 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:55 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2661285888
13:45:55.562 INFO  Funcotator - ------------------------------------------------------------
13:45:55.562 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:55.562 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:55.562 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:55.562 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:55.562 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:55 PM UTC
13:45:55.562 INFO  Funcotator - ------------------------------------------------------------
13:45:55.562 INFO  Funcotator - ------------------------------------------------------------
13:45:55.562 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:55.562 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:55.562 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:55.562 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:55.562 INFO  Funcotator - Deflater: IntelDeflater
13:45:55.562 INFO  Funcotator - Inflater: IntelInflater
13:45:55.562 INFO  Funcotator - GCS max retries/reopens: 20
13:45:55.562 INFO  Funcotator - Requester pays: disabled
13:45:55.562 INFO  Funcotator - Initializing engine
13:45:55.563 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
13:45:55.563 INFO  Funcotator - Done initializing engine
13:45:55.563 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:55.563 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:55.563 INFO  Funcotator - Initializing data sources...
13:45:55.563 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:55.563 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:55.564 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
13:45:55.564 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
13:45:55.564 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
13:45:55.564 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
13:45:55.564 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
13:45:55.565 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
13:45:55.565 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
13:45:55.565 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
13:45:55.565 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
13:45:55.565 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
13:45:55.565 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
13:45:55.565 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:55.566 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
13:45:55.566 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
13:45:55.566 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:55.566 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:55.566 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
13:45:55.566 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
13:45:55.608 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
13:45:55.625 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
13:45:55.632 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
13:45:55.632 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
13:45:55.633 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
13:45:55.633 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
13:45:56.237 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
13:45:56.274 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:56.274 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:56.275 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:56.276 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
13:45:56.359 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:56.359 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:56.360 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
13:45:56.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:56.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:56.387 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
13:45:56.388 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
13:45:56.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:56.388 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:56.389 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
13:45:56.391 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:56.394 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
13:45:56.396 INFO  Funcotator - Initializing Funcotator Engine...
13:45:56.396 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:56.396 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:56.396 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18311204752778185897.vcf
13:45:56.397 INFO  ProgressMeter - Starting traversal
13:45:56.397 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:56.501 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
13:45:56.501 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:56.501 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:56.502 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2661285888
13:45:56.566 INFO  Funcotator - ------------------------------------------------------------
13:45:56.566 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:56.566 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:56.566 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:56.566 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:56.566 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:56 PM UTC
13:45:56.566 INFO  Funcotator - ------------------------------------------------------------
13:45:56.566 INFO  Funcotator - ------------------------------------------------------------
13:45:56.566 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:56.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:56.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:56.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:56.566 INFO  Funcotator - Deflater: IntelDeflater
13:45:56.566 INFO  Funcotator - Inflater: IntelInflater
13:45:56.566 INFO  Funcotator - GCS max retries/reopens: 20
13:45:56.567 INFO  Funcotator - Requester pays: disabled
13:45:56.567 INFO  Funcotator - Initializing engine
13:45:56.567 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
13:45:56.568 INFO  Funcotator - Done initializing engine
13:45:56.568 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:56.568 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:56.568 INFO  Funcotator - Initializing data sources...
13:45:56.568 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:56.568 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:56.568 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:56.568 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
13:45:56.569 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
13:45:56.569 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
13:45:56.569 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
13:45:56.569 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:45:56.569 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:45:56.569 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
13:45:56.570 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
13:45:56.570 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
13:45:56.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:45:56.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:56.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:56.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:56.570 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
13:45:56.570 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:56.570 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:56.571 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
13:45:56.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:56.630 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
13:45:56.636 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
13:45:56.637 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
13:45:56.637 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
13:45:56.637 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
13:45:57.231 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
13:45:57.269 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
13:45:57.269 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:57.270 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
13:45:57.270 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
13:45:57.355 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:57.355 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:57.356 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
13:45:57.383 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:57.383 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:57.383 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
13:45:57.384 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
13:45:57.384 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:57.384 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:57.386 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
13:45:57.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:57.393 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
13:45:57.395 INFO  Funcotator - Initializing Funcotator Engine...
13:45:57.396 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
13:45:57.396 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:57.396 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:57.396 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:57.396 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:57.397 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:57.397 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:57.397 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:57.397 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:57.397 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:57.397 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3729834045060879150.vcf
13:45:57.397 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
13:45:57.398 INFO  ProgressMeter - Starting traversal
13:45:57.398 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:57.424 INFO  ProgressMeter -             unmapped              0.0                     3           6923.1
13:45:57.424 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:57.424 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:57.427 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:57 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2661285888
13:45:57.495 INFO  Funcotator - ------------------------------------------------------------
13:45:57.495 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:57.495 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:57.495 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:57.495 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:57.495 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:57 PM UTC
13:45:57.495 INFO  Funcotator - ------------------------------------------------------------
13:45:57.495 INFO  Funcotator - ------------------------------------------------------------
13:45:57.495 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:57.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:57.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:57.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:57.495 INFO  Funcotator - Deflater: IntelDeflater
13:45:57.495 INFO  Funcotator - Inflater: IntelInflater
13:45:57.495 INFO  Funcotator - GCS max retries/reopens: 20
13:45:57.495 INFO  Funcotator - Requester pays: disabled
13:45:57.495 INFO  Funcotator - Initializing engine
13:45:57.496 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
13:45:57.496 INFO  Funcotator - Done initializing engine
13:45:57.497 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:57.497 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:57.497 INFO  Funcotator - Initializing data sources...
13:45:57.497 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:57.497 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:57.497 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
13:45:57.497 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
13:45:57.497 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
13:45:57.497 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
13:45:57.497 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
13:45:57.498 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
13:45:57.498 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
13:45:57.498 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
13:45:57.498 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
13:45:57.498 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
13:45:57.498 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
13:45:57.498 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:57.499 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
13:45:57.499 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
13:45:57.499 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:57.499 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:57.499 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
13:45:57.499 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
13:45:57.540 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
13:45:57.558 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
13:45:57.564 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
13:45:57.565 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
13:45:57.565 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
13:45:57.565 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
13:45:58.099 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:58.181 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
13:45:58.182 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:58.182 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
13:45:58.183 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
13:45:58.267 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:58.267 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:58.267 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
13:45:58.294 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
13:45:58.295 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:58.295 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
13:45:58.295 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
13:45:58.296 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:58.296 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:58.297 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
13:45:58.300 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:58.302 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
13:45:58.304 INFO  Funcotator - Initializing Funcotator Engine...
13:45:58.304 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:45:58.304 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:58.304 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out230141190065795815.vcf
13:45:58.305 INFO  ProgressMeter - Starting traversal
13:45:58.305 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:58.408 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
13:45:58.408 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:45:58.408 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:45:58.409 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2661285888
13:45:58.479 INFO  Funcotator - ------------------------------------------------------------
13:45:58.479 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:58.479 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:58.479 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:58.479 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:58.479 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:58 PM UTC
13:45:58.479 INFO  Funcotator - ------------------------------------------------------------
13:45:58.479 INFO  Funcotator - ------------------------------------------------------------
13:45:58.479 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:58.479 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:58.479 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:58.479 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:58.479 INFO  Funcotator - Deflater: IntelDeflater
13:45:58.479 INFO  Funcotator - Inflater: IntelInflater
13:45:58.479 INFO  Funcotator - GCS max retries/reopens: 20
13:45:58.479 INFO  Funcotator - Requester pays: disabled
13:45:58.479 INFO  Funcotator - Initializing engine
13:45:58.480 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
13:45:58.481 INFO  Funcotator - Done initializing engine
13:45:58.481 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:58.481 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:58.481 INFO  Funcotator - Initializing data sources...
13:45:58.481 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:58.481 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:58.481 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
13:45:58.481 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
13:45:58.481 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
13:45:58.482 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
13:45:58.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:45:58.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:45:58.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:45:58.482 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
13:45:58.482 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
13:45:58.482 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:58.483 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:45:58.483 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
13:45:58.483 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
13:45:58.483 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
13:45:58.483 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
13:45:58.483 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:58.483 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
13:45:58.484 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
13:45:58.527 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
13:45:58.545 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
13:45:58.552 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
13:45:58.552 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
13:45:58.552 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
13:45:58.553 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
13:45:59.121 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
13:45:59.158 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
13:45:59.158 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:45:59.159 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
13:45:59.159 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
13:45:59.243 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:45:59.243 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:59.244 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
13:45:59.272 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:59.272 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:45:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:45:59.272 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
13:45:59.273 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
13:45:59.273 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:59.273 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:45:59.274 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
13:45:59.276 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:59.278 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
13:45:59.280 INFO  Funcotator - Initializing Funcotator Engine...
13:45:59.280 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
13:45:59.280 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:45:59.280 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:45:59.280 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:45:59.280 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:45:59.280 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:45:59.280 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:45:59.281 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:45:59.281 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:45:59.281 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1444227774281369968.maf
13:45:59.281 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
13:45:59.282 INFO  ProgressMeter - Starting traversal
13:45:59.282 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:45:59.301 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
13:45:59.301 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:45:59.301 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:45:59.301 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:45:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2661285888
13:45:59.371 INFO  Funcotator - ------------------------------------------------------------
13:45:59.371 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:45:59.371 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:45:59.371 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:45:59.371 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:45:59.371 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:45:59 PM UTC
13:45:59.371 INFO  Funcotator - ------------------------------------------------------------
13:45:59.371 INFO  Funcotator - ------------------------------------------------------------
13:45:59.371 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:45:59.371 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:45:59.371 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:45:59.371 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:45:59.371 INFO  Funcotator - Deflater: IntelDeflater
13:45:59.371 INFO  Funcotator - Inflater: IntelInflater
13:45:59.371 INFO  Funcotator - GCS max retries/reopens: 20
13:45:59.371 INFO  Funcotator - Requester pays: disabled
13:45:59.371 INFO  Funcotator - Initializing engine
13:45:59.372 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
13:45:59.372 INFO  Funcotator - Done initializing engine
13:45:59.372 INFO  Funcotator - Skipping sequence dictionary validation.
13:45:59.372 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:45:59.372 INFO  Funcotator - Initializing data sources...
13:45:59.372 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:45:59.372 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:45:59.373 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
13:45:59.373 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
13:45:59.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
13:45:59.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
13:45:59.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:45:59.374 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
13:45:59.374 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
13:45:59.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
13:45:59.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
13:45:59.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:45:59.374 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
13:45:59.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:45:59.375 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:45:59.375 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:45:59.375 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:45:59.375 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:45:59.375 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:45:59.375 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
13:45:59.419 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
13:45:59.437 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
13:45:59.444 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
13:45:59.444 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
13:45:59.445 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
13:45:59.445 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
13:46:00.013 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
13:46:00.052 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
13:46:00.052 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:00.053 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
13:46:00.053 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
13:46:00.137 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:00.138 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:00.138 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
13:46:00.222 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:00.222 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:46:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:00.222 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
13:46:00.223 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
13:46:00.223 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:00.223 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:00.224 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
13:46:00.226 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:00.228 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
13:46:00.230 INFO  Funcotator - Initializing Funcotator Engine...
13:46:00.230 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:00.230 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:00.230 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9443858440799037130.maf
13:46:00.231 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
13:46:00.231 INFO  ProgressMeter - Starting traversal
13:46:00.231 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:00.335 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
13:46:00.335 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:46:00.336 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:46:00.336 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2661285888
13:46:00.406 INFO  Funcotator - ------------------------------------------------------------
13:46:00.406 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:00.406 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:00.406 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:00.406 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:00.406 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:00 PM UTC
13:46:00.406 INFO  Funcotator - ------------------------------------------------------------
13:46:00.406 INFO  Funcotator - ------------------------------------------------------------
13:46:00.406 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:00.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:00.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:00.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:00.406 INFO  Funcotator - Deflater: IntelDeflater
13:46:00.406 INFO  Funcotator - Inflater: IntelInflater
13:46:00.406 INFO  Funcotator - GCS max retries/reopens: 20
13:46:00.406 INFO  Funcotator - Requester pays: disabled
13:46:00.406 INFO  Funcotator - Initializing engine
13:46:00.407 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
13:46:00.407 INFO  Funcotator - Done initializing engine
13:46:00.407 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:00.407 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:00.408 INFO  Funcotator - Initializing data sources...
13:46:00.408 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:00.408 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:00.408 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
13:46:00.408 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
13:46:00.408 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
13:46:00.408 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
13:46:00.409 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
13:46:00.409 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
13:46:00.409 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
13:46:00.409 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
13:46:00.409 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
13:46:00.409 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:46:00.409 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
13:46:00.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:00.410 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
13:46:00.410 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
13:46:00.410 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
13:46:00.410 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:00.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:46:00.410 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
13:46:00.453 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
13:46:00.472 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
13:46:00.478 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:46:00.479 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
13:46:00.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:46:00.479 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
13:46:01.091 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
13:46:01.128 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
13:46:01.128 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:01.129 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
13:46:01.130 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:46:01.213 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:01.214 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:01.214 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
13:46:01.241 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:01.241 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:46:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:01.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
13:46:01.242 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:46:01.243 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:01.243 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:01.243 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:01.245 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:01.248 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:01.250 INFO  Funcotator - Initializing Funcotator Engine...
13:46:01.250 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
13:46:01.250 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:46:01.250 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:46:01.250 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:46:01.250 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:46:01.251 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:46:01.251 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:01.251 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8521480090729080986.maf
13:46:01.251 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
13:46:01.252 INFO  ProgressMeter - Starting traversal
13:46:01.252 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:01.270 INFO  ProgressMeter -             unmapped              0.0                     3          10000.0
13:46:01.270 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
13:46:01.271 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:46:01.271 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2703228928
13:46:01.336 INFO  Funcotator - ------------------------------------------------------------
13:46:01.336 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:01.336 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:01.336 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:01.336 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:01.336 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:01 PM UTC
13:46:01.336 INFO  Funcotator - ------------------------------------------------------------
13:46:01.336 INFO  Funcotator - ------------------------------------------------------------
13:46:01.336 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:01.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:01.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:01.336 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:01.336 INFO  Funcotator - Deflater: IntelDeflater
13:46:01.336 INFO  Funcotator - Inflater: IntelInflater
13:46:01.336 INFO  Funcotator - GCS max retries/reopens: 20
13:46:01.336 INFO  Funcotator - Requester pays: disabled
13:46:01.336 INFO  Funcotator - Initializing engine
13:46:01.337 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
13:46:01.337 INFO  Funcotator - Done initializing engine
13:46:01.337 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:01.338 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:01.338 INFO  Funcotator - Initializing data sources...
13:46:01.338 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:01.338 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:01.338 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
13:46:01.338 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
13:46:01.353 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
13:46:01.354 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
13:46:01.354 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:46:01.354 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:46:01.354 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:46:01.354 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
13:46:01.354 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
13:46:01.354 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
13:46:01.355 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
13:46:01.355 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:01.355 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
13:46:01.355 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
13:46:01.355 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:01.355 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:01.355 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
13:46:01.356 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
13:46:01.397 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
13:46:01.415 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
13:46:01.421 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
13:46:01.422 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
13:46:01.422 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
13:46:01.422 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
13:46:02.034 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
13:46:02.072 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:46:02.072 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.073 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
13:46:02.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:46:02.157 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:02.157 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:02.158 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
13:46:02.185 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:02.185 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:46:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:02.185 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
13:46:02.186 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
13:46:02.186 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:02.186 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:02.187 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
13:46:02.189 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:02.192 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
13:46:02.194 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.194 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:02.194 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:02.194 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out2010854355157639587.maf
13:46:02.194 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
13:46:02.194 INFO  ProgressMeter - Starting traversal
13:46:02.194 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.297 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
13:46:02.297 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
13:46:02.297 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
13:46:02.298 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2703228928
13:46:02.362 INFO  Funcotator - ------------------------------------------------------------
13:46:02.362 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:02.362 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:02.362 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:02.362 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:02.362 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:02 PM UTC
13:46:02.362 INFO  Funcotator - ------------------------------------------------------------
13:46:02.362 INFO  Funcotator - ------------------------------------------------------------
13:46:02.362 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:02.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:02.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:02.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:02.362 INFO  Funcotator - Deflater: IntelDeflater
13:46:02.362 INFO  Funcotator - Inflater: IntelInflater
13:46:02.362 INFO  Funcotator - GCS max retries/reopens: 20
13:46:02.362 INFO  Funcotator - Requester pays: disabled
13:46:02.362 INFO  Funcotator - Initializing engine
13:46:02.363 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
13:46:02.385 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
13:46:02.385 INFO  Funcotator - Done initializing engine
13:46:02.385 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:02.385 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:02.385 INFO  Funcotator - Initializing data sources...
13:46:02.385 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/
13:46:02.385 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:02.386 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
13:46:02.386 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
13:46:02.386 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
13:46:02.386 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:02.386 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
13:46:02.386 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.387 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
13:46:02.387 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
13:46:02.388 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
13:46:02.388 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:02.389 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
13:46:02.402 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/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:46:02.412 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
13:46:02.420 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.425 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:02.425 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16532175243177231733.vcf
13:46:02.441 INFO  ProgressMeter - Starting traversal
13:46:02.441 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.454 INFO  ProgressMeter -             unmapped              0.0                    32         147692.3
13:46:02.454 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
13:46:02.454 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:02.462 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:02.531 INFO  Funcotator - ------------------------------------------------------------
13:46:02.531 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:02.531 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:02.531 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:02.531 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:02.531 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:02 PM UTC
13:46:02.531 INFO  Funcotator - ------------------------------------------------------------
13:46:02.531 INFO  Funcotator - ------------------------------------------------------------
13:46:02.531 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:02.531 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:02.531 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:02.531 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:02.531 INFO  Funcotator - Deflater: IntelDeflater
13:46:02.531 INFO  Funcotator - Inflater: IntelInflater
13:46:02.531 INFO  Funcotator - GCS max retries/reopens: 20
13:46:02.531 INFO  Funcotator - Requester pays: disabled
13:46:02.531 INFO  Funcotator - Initializing engine
13:46:02.532 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
13:46:02.553 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
13:46:02.553 INFO  Funcotator - Done initializing engine
13:46:02.553 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:02.553 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:02.553 INFO  Funcotator - Initializing data sources...
13:46:02.553 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/
13:46:02.553 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:02.554 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
13:46:02.554 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
13:46:02.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:46:02.554 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:02.554 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
13:46:02.554 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.555 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
13:46:02.555 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
13:46:02.555 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
13:46:02.555 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:02.556 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
13:46:02.564 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
13:46:02.572 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
13:46:02.580 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.584 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:02.585 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6778341228714375341.vcf
13:46:02.597 INFO  ProgressMeter - Starting traversal
13:46:02.597 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.608 INFO  ProgressMeter -             unmapped              0.0                    32         174545.5
13:46:02.608 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
13:46:02.608 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:02.613 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:02.614 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16532175243177231733.vcf
13:46:02.624 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6778341228714375341.vcf
13:46:02.702 INFO  Funcotator - ------------------------------------------------------------
13:46:02.702 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:02.702 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:02.702 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:02.702 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:02.702 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:02 PM UTC
13:46:02.702 INFO  Funcotator - ------------------------------------------------------------
13:46:02.702 INFO  Funcotator - ------------------------------------------------------------
13:46:02.703 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:02.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:02.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:02.703 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:02.703 INFO  Funcotator - Deflater: IntelDeflater
13:46:02.703 INFO  Funcotator - Inflater: IntelInflater
13:46:02.703 INFO  Funcotator - GCS max retries/reopens: 20
13:46:02.703 INFO  Funcotator - Requester pays: disabled
13:46:02.703 INFO  Funcotator - Initializing engine
13:46:02.704 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
13:46:02.705 INFO  Funcotator - Done initializing engine
13:46:02.705 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:02.705 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:02.705 INFO  Funcotator - Initializing data sources...
13:46:02.705 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:02.705 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:02.705 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
13:46:02.705 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
13:46:02.705 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
13:46:02.705 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:02.705 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
13:46:02.705 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.706 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
13:46:02.706 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
13:46:02.706 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
13:46:02.706 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:02.707 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
13:46:02.708 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
13:46:02.765 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
13:46:02.766 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.766 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:02.766 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.
13:46:02.766 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1545517705990174519.maf
13:46:02.767 INFO  ProgressMeter - Starting traversal
13:46:02.767 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.769 WARN  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
13:46:02.769 WARN  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
13:46:02.769 WARN  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
13:46:02.771 WARN  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=
13:46:02.771 WARN  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=
13:46:02.772 WARN  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=
13:46:02.772 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
13:46:02.772 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
13:46:02.772 WARN  Funcotator - ================================================================================
13:46:02.772 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:02.772 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:02.772 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:02.772 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:02.772 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:02.772 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:02.772 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:02.772 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:02.772 WARN  Funcotator -  run was misconfigured.     
13:46:02.772 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:02.772 WARN  Funcotator - ================================================================================
13:46:02.772 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:02.772 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:02.843 INFO  Funcotator - ------------------------------------------------------------
13:46:02.843 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:02.843 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:02.843 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:02.843 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:02.843 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:02 PM UTC
13:46:02.843 INFO  Funcotator - ------------------------------------------------------------
13:46:02.843 INFO  Funcotator - ------------------------------------------------------------
13:46:02.843 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:02.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:02.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:02.843 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:02.843 INFO  Funcotator - Deflater: IntelDeflater
13:46:02.843 INFO  Funcotator - Inflater: IntelInflater
13:46:02.843 INFO  Funcotator - GCS max retries/reopens: 20
13:46:02.843 INFO  Funcotator - Requester pays: disabled
13:46:02.843 INFO  Funcotator - Initializing engine
13:46:02.844 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
13:46:02.845 INFO  Funcotator - Done initializing engine
13:46:02.845 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:02.845 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:02.845 INFO  Funcotator - Initializing data sources...
13:46:02.845 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:02.845 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:02.845 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
13:46:02.845 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
13:46:02.845 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
13:46:02.845 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:02.845 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
13:46:02.845 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.846 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
13:46:02.846 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
13:46:02.846 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
13:46:02.846 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:02.847 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
13:46:02.847 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
13:46:02.848 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
13:46:02.849 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.849 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:02.849 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.
13:46:02.849 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15831609472413634196.maf
13:46:02.849 INFO  ProgressMeter - Starting traversal
13:46:02.849 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.851 WARN  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
13:46:02.851 WARN  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
13:46:02.852 WARN  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
13:46:02.853 WARN  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=
13:46:02.853 WARN  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=
13:46:02.854 WARN  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=
13:46:02.854 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
13:46:02.854 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
13:46:02.854 WARN  Funcotator - ================================================================================
13:46:02.854 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:02.854 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:02.854 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:02.854 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:02.854 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:02.854 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:02.854 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:02.854 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:02.854 WARN  Funcotator -  run was misconfigured.     
13:46:02.854 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:02.854 WARN  Funcotator - ================================================================================
13:46:02.854 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:02.855 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:02.922 INFO  Funcotator - ------------------------------------------------------------
13:46:02.922 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:02.922 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:02.922 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:02.922 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:02.922 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:02 PM UTC
13:46:02.922 INFO  Funcotator - ------------------------------------------------------------
13:46:02.922 INFO  Funcotator - ------------------------------------------------------------
13:46:02.922 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:02.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:02.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:02.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:02.922 INFO  Funcotator - Deflater: IntelDeflater
13:46:02.922 INFO  Funcotator - Inflater: IntelInflater
13:46:02.922 INFO  Funcotator - GCS max retries/reopens: 20
13:46:02.922 INFO  Funcotator - Requester pays: disabled
13:46:02.922 INFO  Funcotator - Initializing engine
13:46:02.923 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
13:46:02.924 INFO  Funcotator - Done initializing engine
13:46:02.924 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:02.924 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:02.924 INFO  Funcotator - Initializing data sources...
13:46:02.924 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:02.924 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:02.925 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
13:46:02.925 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
13:46:02.925 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
13:46:02.925 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:02.925 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
13:46:02.925 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:02.925 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
13:46:02.926 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
13:46:02.926 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
13:46:02.926 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:02.926 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
13:46:02.927 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
13:46:02.928 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
13:46:02.929 INFO  Funcotator - Initializing Funcotator Engine...
13:46:02.929 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:02.929 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.
13:46:02.929 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6591152784660094304.maf
13:46:02.929 INFO  ProgressMeter - Starting traversal
13:46:02.929 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:02.931 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 @ 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
13:46:02.932 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 @ 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
13:46:02.932 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 @ 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
13:46:02.934 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 @ 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=
13:46:02.934 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 @ 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=
13:46:02.936 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 @ 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=
13:46:02.936 INFO  ProgressMeter -             unmapped              0.0                     6          51428.6
13:46:02.936 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
13:46:02.936 WARN  Funcotator - ================================================================================
13:46:02.936 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:02.936 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:02.936 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:02.936 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:02.936 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:02.936 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:02.936 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:02.936 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:02.936 WARN  Funcotator -  run was misconfigured.     
13:46:02.936 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:02.936 WARN  Funcotator - ================================================================================
13:46:02.936 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:02.936 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.007 INFO  Funcotator - ------------------------------------------------------------
13:46:03.007 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.007 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.007 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.007 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.007 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.007 INFO  Funcotator - ------------------------------------------------------------
13:46:03.007 INFO  Funcotator - ------------------------------------------------------------
13:46:03.008 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.008 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.008 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.008 INFO  Funcotator - Inflater: IntelInflater
13:46:03.008 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.008 INFO  Funcotator - Requester pays: disabled
13:46:03.008 INFO  Funcotator - Initializing engine
13:46:03.009 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
13:46:03.010 INFO  Funcotator - Done initializing engine
13:46:03.010 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:03.010 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:03.010 INFO  Funcotator - Initializing data sources...
13:46:03.010 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:03.010 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:03.010 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
13:46:03.010 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
13:46:03.010 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:03.010 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:03.010 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
13:46:03.010 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:03.011 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
13:46:03.011 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
13:46:03.011 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:03.012 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:03.012 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
13:46:03.013 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
13:46:03.014 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
13:46:03.014 INFO  Funcotator - Initializing Funcotator Engine...
13:46:03.014 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:03.015 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.
13:46:03.015 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14724225216883457301.maf
13:46:03.015 INFO  ProgressMeter - Starting traversal
13:46:03.015 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:03.016 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
13:46:03.017 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
13:46:03.017 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
13:46:03.018 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
13:46:03.018 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
13:46:03.019 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
13:46:03.020 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
13:46:03.020 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
13:46:03.020 WARN  Funcotator - ================================================================================
13:46:03.020 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:03.020 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:03.020 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:03.020 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:03.020 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:03.020 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:03.020 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:03.020 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:03.020 WARN  Funcotator -  run was misconfigured.     
13:46:03.020 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:03.020 WARN  Funcotator - ================================================================================
13:46:03.020 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:03.020 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.090 INFO  Funcotator - ------------------------------------------------------------
13:46:03.090 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.090 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.090 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.090 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.090 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.090 INFO  Funcotator - ------------------------------------------------------------
13:46:03.090 INFO  Funcotator - ------------------------------------------------------------
13:46:03.090 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.090 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.090 INFO  Funcotator - Inflater: IntelInflater
13:46:03.090 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.090 INFO  Funcotator - Requester pays: disabled
13:46:03.090 INFO  Funcotator - Initializing engine
13:46:03.090 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
13:46:03.092 INFO  Funcotator - Done initializing engine
13:46:03.092 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:03.092 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:03.092 INFO  Funcotator - Initializing data sources...
13:46:03.092 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:03.092 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:03.092 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
13:46:03.092 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
13:46:03.092 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
13:46:03.092 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:03.092 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
13:46:03.092 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:03.093 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
13:46:03.093 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
13:46:03.093 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
13:46:03.093 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:03.094 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
13:46:03.094 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
13:46:03.095 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
13:46:03.096 INFO  Funcotator - Initializing Funcotator Engine...
13:46:03.096 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:03.096 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.
13:46:03.096 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3232112074918967784.vcf
13:46:03.103 INFO  ProgressMeter - Starting traversal
13:46:03.103 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:03.117 INFO  ProgressMeter -             unmapped              0.0                    21          90000.0
13:46:03.117 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
13:46:03.117 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:46:03.120 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.121 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3232112074918967784.vcf
13:46:03.190 INFO  Funcotator - ------------------------------------------------------------
13:46:03.190 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.190 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.190 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.190 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.190 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.190 INFO  Funcotator - ------------------------------------------------------------
13:46:03.190 INFO  Funcotator - ------------------------------------------------------------
13:46:03.190 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.190 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.190 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.190 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.190 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.190 INFO  Funcotator - Inflater: IntelInflater
13:46:03.190 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.190 INFO  Funcotator - Requester pays: disabled
13:46:03.190 INFO  Funcotator - Initializing engine
13:46:03.192 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
13:46:03.192 INFO  Funcotator - Done initializing engine
13:46:03.192 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:03.192 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:03.193 INFO  Funcotator - Initializing data sources...
13:46:03.193 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:03.193 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:03.193 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
13:46:03.193 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
13:46:03.193 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
13:46:03.193 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:03.193 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
13:46:03.193 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:03.194 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
13:46:03.194 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
13:46:03.194 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
13:46:03.194 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:03.195 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
13:46:03.195 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
13:46:03.196 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
13:46:03.197 INFO  Funcotator - Initializing Funcotator Engine...
13:46:03.197 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:03.197 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.
13:46:03.197 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3524269482202184755.maf
13:46:03.198 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:03.198 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.264 INFO  Funcotator - ------------------------------------------------------------
13:46:03.264 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.264 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.264 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.264 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.264 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.264 INFO  Funcotator - ------------------------------------------------------------
13:46:03.264 INFO  Funcotator - ------------------------------------------------------------
13:46:03.264 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.264 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.264 INFO  Funcotator - Inflater: IntelInflater
13:46:03.264 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.264 INFO  Funcotator - Requester pays: disabled
13:46:03.264 INFO  Funcotator - Initializing engine
13:46:03.265 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
13:46:03.276 INFO  Funcotator - Done initializing engine
13:46:03.276 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:03.276 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:03.276 INFO  Funcotator - Initializing data sources...
13:46:03.276 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:03.276 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:03.277 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
13:46:03.277 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
13:46:03.277 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
13:46:03.277 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:03.277 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
13:46:03.277 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:03.277 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
13:46:03.278 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
13:46:03.278 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
13:46:03.278 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:03.278 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
13:46:03.286 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
13:46:03.294 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
13:46:03.301 INFO  Funcotator - Initializing Funcotator Engine...
13:46:03.308 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:03.308 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8125755841965176325.maf
13:46:03.308 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
13:46:03.308 INFO  ProgressMeter - Starting traversal
13:46:03.308 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:03.310 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)
13:46:03.311 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)
13:46:03.311 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.311 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:46:03.311 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
13:46:03.311 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
13:46:03.312 WARN  MafOutputRenderer - 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+
13:46:03.316 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.316 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:46:03.316 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
13:46:03.316 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
13:46:03.316 WARN  MafOutputRenderer - 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+
13:46:03.316 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)
13:46:03.317 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)
13:46:03.317 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.317 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:46:03.317 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
13:46:03.317 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
13:46:03.317 WARN  MafOutputRenderer - 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+
13:46:03.317 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)
13:46:03.318 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)
13:46:03.318 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
13:46:03.318 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
13:46:03.318 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
13:46:03.318 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
13:46:03.318 WARN  MafOutputRenderer - 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+
13:46:03.319 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.319 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:46:03.319 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
13:46:03.319 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
13:46:03.319 WARN  MafOutputRenderer - 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+
13:46:03.320 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.320 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:46:03.320 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
13:46:03.320 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
13:46:03.320 WARN  MafOutputRenderer - 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=
13:46:03.320 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)
13:46:03.321 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)
13:46:03.321 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
13:46:03.321 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:46:03.321 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
13:46:03.321 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
13:46:03.321 WARN  MafOutputRenderer - 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=
13:46:03.321 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)
13:46:03.322 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)
13:46:03.322 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.322 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:46:03.322 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
13:46:03.322 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
13:46:03.322 WARN  MafOutputRenderer - 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+
13:46:03.323 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
13:46:03.323 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
13:46:03.323 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
13:46:03.323 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
13:46:03.323 WARN  MafOutputRenderer - 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+
13:46:03.323 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)
13:46:03.324 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)
13:46:03.324 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
13:46:03.324 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
13:46:03.324 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
13:46:03.324 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
13:46:03.324 WARN  MafOutputRenderer - 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=
13:46:03.325 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
13:46:03.325 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
13:46:03.325 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
13:46:03.325 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.461 INFO  Funcotator - ------------------------------------------------------------
13:46:03.461 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.461 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.461 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.462 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.462 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.462 INFO  Funcotator - ------------------------------------------------------------
13:46:03.462 INFO  Funcotator - ------------------------------------------------------------
13:46:03.462 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.462 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.462 INFO  Funcotator - Inflater: IntelInflater
13:46:03.462 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.462 INFO  Funcotator - Requester pays: disabled
13:46:03.462 INFO  Funcotator - Initializing engine
13:46:03.463 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
13:46:03.465 INFO  Funcotator - Done initializing engine
13:46:03.465 INFO  Funcotator - Validating sequence dictionaries...
13:46:03.465 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2703228928
13:46:03.527 INFO  Funcotator - ------------------------------------------------------------
13:46:03.527 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:03.527 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:03.527 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:03.527 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:03.527 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:03 PM UTC
13:46:03.527 INFO  Funcotator - ------------------------------------------------------------
13:46:03.527 INFO  Funcotator - ------------------------------------------------------------
13:46:03.527 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:03.527 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:03.527 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:03.527 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:03.527 INFO  Funcotator - Deflater: IntelDeflater
13:46:03.527 INFO  Funcotator - Inflater: IntelInflater
13:46:03.527 INFO  Funcotator - GCS max retries/reopens: 20
13:46:03.527 INFO  Funcotator - Requester pays: disabled
13:46:03.527 INFO  Funcotator - Initializing engine
13:46:03.529 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
13:46:03.530 INFO  Funcotator - Done initializing engine
13:46:03.530 INFO  Funcotator - Validating sequence dictionaries...
13:46:03.530 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:03.530 INFO  Funcotator - Initializing data sources...
13:46:03.530 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:03.530 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:03.531 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
13:46:03.531 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
13:46:03.531 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
13:46:03.531 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
13:46:03.531 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
13:46:03.531 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
13:46:03.531 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 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
13:46:03.532 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:03.532 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
13:46:03.533 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
13:46:03.576 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
13:46:03.593 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
13:46:03.600 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
13:46:03.600 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
13:46:03.600 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:46:03.601 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
13:46:04.240 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
13:46:04.277 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
13:46:04.277 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:04.278 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
13:46:04.278 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
13:46:04.361 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:04.361 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:04.361 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
13:46:04.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:04.388 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:46:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:04.389 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
13:46:04.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:46:04.390 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:04.390 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:04.390 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
13:46:04.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:04.395 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
13:46:04.396 INFO  Funcotator - Initializing Funcotator Engine...
13:46:04.397 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:46:04.397 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.
13:46:04.397 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator17619652625178291167.vcf
13:46:04.398 INFO  ProgressMeter - Starting traversal
13:46:04.398 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:06.437 INFO  ProgressMeter -             unmapped              0.0                   198           5826.4
13:46:06.437 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:46:06.437 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:46:06.445 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:06 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2799697920
13:46:06.510 INFO  Funcotator - ------------------------------------------------------------
13:46:06.510 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:06.510 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:06.510 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:06.510 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:06.510 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:06 PM UTC
13:46:06.510 INFO  Funcotator - ------------------------------------------------------------
13:46:06.510 INFO  Funcotator - ------------------------------------------------------------
13:46:06.510 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:06.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:06.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:06.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:06.510 INFO  Funcotator - Deflater: IntelDeflater
13:46:06.510 INFO  Funcotator - Inflater: IntelInflater
13:46:06.510 INFO  Funcotator - GCS max retries/reopens: 20
13:46:06.510 INFO  Funcotator - Requester pays: disabled
13:46:06.510 INFO  Funcotator - Initializing engine
13:46:06.512 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
13:46:06.513 INFO  Funcotator - Done initializing engine
13:46:06.513 INFO  Funcotator - Validating sequence dictionaries...
13:46:06.513 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:06.513 INFO  Funcotator - Initializing data sources...
13:46:06.513 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:06.513 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:06.514 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
13:46:06.514 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
13:46:06.514 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
13:46:06.514 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
13:46:06.514 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
13:46:06.514 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
13:46:06.514 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
13:46:06.514 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
13:46:06.515 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
13:46:06.515 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
13:46:06.515 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
13:46:06.515 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:06.515 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
13:46:06.515 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
13:46:06.515 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:06.515 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:06.515 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
13:46:06.516 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
13:46:06.557 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
13:46:06.575 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
13:46:06.582 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
13:46:06.582 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
13:46:06.582 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
13:46:06.583 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
13:46:07.196 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
13:46:07.233 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
13:46:07.233 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:07.234 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
13:46:07.234 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
13:46:07.318 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:07.318 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:07.319 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
13:46:07.346 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:07.346 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:46:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:07.346 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
13:46:07.347 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
13:46:07.347 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:07.347 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:07.348 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
13:46:07.350 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:07.352 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
13:46:07.354 INFO  Funcotator - Initializing Funcotator Engine...
13:46:07.354 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
13:46:07.354 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.
13:46:07.354 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator10204625409212864537.maf
13:46:07.354 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
13:46:07.355 INFO  ProgressMeter - Starting traversal
13:46:07.355 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:09.338 INFO  ProgressMeter -             unmapped              0.0                   198           5990.9
13:46:09.338 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
13:46:09.338 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
13:46:09.338 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:09 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2847932416
13:46:09.412 INFO  Funcotator - ------------------------------------------------------------
13:46:09.412 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:09.412 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:09.412 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:09.412 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:09.412 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:09 PM UTC
13:46:09.412 INFO  Funcotator - ------------------------------------------------------------
13:46:09.412 INFO  Funcotator - ------------------------------------------------------------
13:46:09.412 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:09.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:09.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:09.412 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:09.412 INFO  Funcotator - Deflater: IntelDeflater
13:46:09.412 INFO  Funcotator - Inflater: IntelInflater
13:46:09.412 INFO  Funcotator - GCS max retries/reopens: 20
13:46:09.412 INFO  Funcotator - Requester pays: disabled
13:46:09.412 INFO  Funcotator - Initializing engine
13:46:09.441 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
13:46:09.462 INFO  Funcotator - Done initializing engine
13:46:09.462 INFO  Funcotator - Validating sequence dictionaries...
13:46:09.469 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:09.469 INFO  Funcotator - Initializing data sources...
13:46:09.469 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:09.469 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:09.470 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
13:46:09.470 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
13:46:09.470 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
13:46:09.470 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
13:46:09.470 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
13:46:09.470 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
13:46:09.471 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
13:46:09.471 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
13:46:09.471 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
13:46:09.471 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
13:46:09.471 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
13:46:09.471 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/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
13:46:09.471 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
13:46:09.472 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:09.472 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
13:46:09.528 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
13:46:09.546 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
13:46:09.553 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
13:46:09.553 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
13:46:09.553 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
13:46:09.553 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
13:46:10.118 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
13:46:10.211 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
13:46:10.211 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.212 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
13:46:10.212 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
13:46:10.213 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
13:46:10.213 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
13:46:10.214 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
13:46:10.214 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:10.214 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
13:46:10.216 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
13:46:10.217 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
13:46:10.218 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.222 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:10.222 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator6562033072377277940.vcf
13:46:10.223 INFO  ProgressMeter - Starting traversal
13:46:10.223 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.228 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
13:46:10.231 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2847932416
13:46:10.297 INFO  Funcotator - ------------------------------------------------------------
13:46:10.297 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.297 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.297 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.297 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.297 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.297 INFO  Funcotator - ------------------------------------------------------------
13:46:10.297 INFO  Funcotator - ------------------------------------------------------------
13:46:10.297 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.297 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.297 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.297 INFO  Funcotator - Inflater: IntelInflater
13:46:10.297 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.297 INFO  Funcotator - Requester pays: disabled
13:46:10.297 INFO  Funcotator - Initializing engine
13:46:10.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
13:46:10.300 INFO  Funcotator - Done initializing engine
13:46:10.300 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.300 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.300 INFO  Funcotator - Initializing data sources...
13:46:10.300 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
13:46:10.300 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.300 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
13:46:10.300 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
13:46:10.300 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
13:46:10.300 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.300 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
13:46:10.300 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.301 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
13:46:10.301 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
13:46:10.302 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
13:46:10.302 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
13:46:10.302 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
13:46:10.302 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
13:46:10.303 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
13:46:10.303 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.303 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.303 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.
13:46:10.303 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.303 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing16059295006340666893.vcf
13:46:10.304 INFO  ProgressMeter - Starting traversal
13:46:10.304 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.308 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
13:46:10.308 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:46:10.308 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
13:46:10.310 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.311 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing16059295006340666893.vcf
13:46:10.377 INFO  Funcotator - ------------------------------------------------------------
13:46:10.377 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.377 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.377 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.377 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.377 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.377 INFO  Funcotator - ------------------------------------------------------------
13:46:10.377 INFO  Funcotator - ------------------------------------------------------------
13:46:10.377 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.377 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.377 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.377 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.377 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.377 INFO  Funcotator - Inflater: IntelInflater
13:46:10.377 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.377 INFO  Funcotator - Requester pays: disabled
13:46:10.377 INFO  Funcotator - Initializing engine
13:46:10.378 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
13:46:10.379 INFO  Funcotator - Done initializing engine
13:46:10.379 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.379 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.379 INFO  Funcotator - Initializing data sources...
13:46:10.379 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.379 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.379 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
13:46:10.379 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
13:46:10.379 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
13:46:10.379 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.379 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
13:46:10.379 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.380 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
13:46:10.380 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
13:46:10.380 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
13:46:10.380 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.381 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
13:46:10.382 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
13:46:10.383 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/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:10.383 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.383 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.383 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.
13:46:10.384 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3128699216822331042.maf
13:46:10.384 INFO  ProgressMeter - Starting traversal
13:46:10.384 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.386 WARN  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=
13:46:10.387 WARN  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=
13:46:10.387 WARN  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=
13:46:10.388 WARN  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=
13:46:10.388 WARN  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=
13:46:10.388 WARN  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=
13:46:10.389 WARN  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=
13:46:10.389 WARN  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=
13:46:10.390 WARN  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=
13:46:10.390 WARN  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=
13:46:10.390 WARN  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=
13:46:10.391 WARN  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=
13:46:10.391 WARN  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=
13:46:10.391 WARN  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=
13:46:10.391 WARN  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=
13:46:10.392 WARN  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=
13:46:10.392 WARN  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=
13:46:10.392 WARN  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=
13:46:10.392 WARN  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=
13:46:10.393 WARN  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=
13:46:10.393 WARN  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=
13:46:10.393 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
13:46:10.393 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
13:46:10.393 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:46:10.393 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.398 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
13:46:10.399 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
13:46:10.472 INFO  Funcotator - ------------------------------------------------------------
13:46:10.472 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.472 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.473 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.473 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.473 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.473 INFO  Funcotator - ------------------------------------------------------------
13:46:10.473 INFO  Funcotator - ------------------------------------------------------------
13:46:10.473 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.473 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.473 INFO  Funcotator - Inflater: IntelInflater
13:46:10.473 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.473 INFO  Funcotator - Requester pays: disabled
13:46:10.473 INFO  Funcotator - Initializing engine
13:46:10.473 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
13:46:10.475 INFO  Funcotator - Done initializing engine
13:46:10.475 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.475 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.475 INFO  Funcotator - Initializing data sources...
13:46:10.475 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.475 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.475 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
13:46:10.475 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
13:46:10.475 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
13:46:10.475 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.475 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
13:46:10.475 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.476 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
13:46:10.476 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
13:46:10.476 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
13:46:10.476 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.477 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
13:46:10.477 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
13:46:10.478 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
13:46:10.479 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.479 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.479 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.
13:46:10.479 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1586024568022699427.vcf
13:46:10.483 INFO  ProgressMeter - Starting traversal
13:46:10.483 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.491 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
13:46:10.491 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
13:46:10.491 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:46:10.493 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.494 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1586024568022699427.vcf
13:46:10.566 INFO  Funcotator - ------------------------------------------------------------
13:46:10.566 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.566 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.566 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.566 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.566 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.566 INFO  Funcotator - ------------------------------------------------------------
13:46:10.566 INFO  Funcotator - ------------------------------------------------------------
13:46:10.566 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.566 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.566 INFO  Funcotator - Inflater: IntelInflater
13:46:10.566 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.566 INFO  Funcotator - Requester pays: disabled
13:46:10.566 INFO  Funcotator - Initializing engine
13:46:10.567 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
13:46:10.568 INFO  Funcotator - Done initializing engine
13:46:10.568 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.568 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.568 INFO  Funcotator - Initializing data sources...
13:46:10.568 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.568 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.568 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
13:46:10.568 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
13:46:10.568 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
13:46:10.568 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.569 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
13:46:10.569 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.569 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
13:46:10.569 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
13:46:10.570 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
13:46:10.570 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.570 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
13:46:10.571 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
13:46:10.573 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
13:46:10.573 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.573 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.573 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.
13:46:10.573 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.573 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13263833890751530292.vcf
13:46:10.574 INFO  ProgressMeter - Starting traversal
13:46:10.574 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.578 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
13:46:10.579 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
13:46:10.579 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:46:10.581 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.581 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13263833890751530292.vcf
13:46:10.651 INFO  Funcotator - ------------------------------------------------------------
13:46:10.652 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.652 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.652 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.652 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.652 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.652 INFO  Funcotator - ------------------------------------------------------------
13:46:10.652 INFO  Funcotator - ------------------------------------------------------------
13:46:10.652 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.652 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.652 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.652 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.652 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.652 INFO  Funcotator - Inflater: IntelInflater
13:46:10.652 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.652 INFO  Funcotator - Requester pays: disabled
13:46:10.652 INFO  Funcotator - Initializing engine
13:46:10.653 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
13:46:10.653 INFO  Funcotator - Done initializing engine
13:46:10.653 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.653 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.653 INFO  Funcotator - Initializing data sources...
13:46:10.653 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.653 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.654 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
13:46:10.654 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
13:46:10.654 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
13:46:10.654 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.654 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
13:46:10.654 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.654 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
13:46:10.655 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
13:46:10.655 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
13:46:10.655 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.655 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
13:46:10.656 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
13:46:10.657 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
13:46:10.658 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.658 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.658 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.
13:46:10.658 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.658 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11189312406016589958.vcf
13:46:10.659 INFO  ProgressMeter - Starting traversal
13:46:10.659 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.666 INFO  ProgressMeter -             unmapped              0.0                    15         128571.4
13:46:10.666 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
13:46:10.666 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
13:46:10.668 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.737 INFO  Funcotator - ------------------------------------------------------------
13:46:10.737 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.737 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.737 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.737 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.737 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.737 INFO  Funcotator - ------------------------------------------------------------
13:46:10.737 INFO  Funcotator - ------------------------------------------------------------
13:46:10.737 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.737 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.737 INFO  Funcotator - Inflater: IntelInflater
13:46:10.737 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.737 INFO  Funcotator - Requester pays: disabled
13:46:10.737 INFO  Funcotator - Initializing engine
13:46:10.738 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
13:46:10.738 INFO  Funcotator - Done initializing engine
13:46:10.738 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.738 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.738 INFO  Funcotator - Initializing data sources...
13:46:10.738 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.738 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.738 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
13:46:10.738 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
13:46:10.739 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
13:46:10.739 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.739 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
13:46:10.739 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.739 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
13:46:10.739 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
13:46:10.740 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
13:46:10.740 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.740 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
13:46:10.741 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
13:46:10.742 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
13:46:10.743 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.743 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.743 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.
13:46:10.743 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.743 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6874810218698797607.maf
13:46:10.743 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
13:46:10.743 INFO  ProgressMeter - Starting traversal
13:46:10.743 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.745 WARN  MafOutputRenderer - 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=
13:46:10.746 WARN  MafOutputRenderer - 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=
13:46:10.747 WARN  MafOutputRenderer - 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=
13:46:10.747 WARN  MafOutputRenderer - 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=
13:46:10.748 WARN  MafOutputRenderer - 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=
13:46:10.748 WARN  MafOutputRenderer - 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=
13:46:10.748 WARN  MafOutputRenderer - 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=
13:46:10.749 WARN  MafOutputRenderer - 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=
13:46:10.749 WARN  MafOutputRenderer - 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=
13:46:10.749 WARN  MafOutputRenderer - 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=
13:46:10.750 WARN  MafOutputRenderer - 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=
13:46:10.750 WARN  MafOutputRenderer - 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=
13:46:10.751 WARN  MafOutputRenderer - 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=
13:46:10.751 WARN  MafOutputRenderer - 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=
13:46:10.751 WARN  MafOutputRenderer - 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=
13:46:10.751 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
13:46:10.751 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
13:46:10.751 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
13:46:10.752 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.752 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11189312406016589958.vcf
13:46:10.823 INFO  Funcotator - ------------------------------------------------------------
13:46:10.823 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.823 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.823 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.823 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.823 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.823 INFO  Funcotator - ------------------------------------------------------------
13:46:10.823 INFO  Funcotator - ------------------------------------------------------------
13:46:10.823 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.823 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.823 INFO  Funcotator - Inflater: IntelInflater
13:46:10.823 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.823 INFO  Funcotator - Requester pays: disabled
13:46:10.823 INFO  Funcotator - Initializing engine
13:46:10.825 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
13:46:10.825 INFO  Funcotator - Done initializing engine
13:46:10.825 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.825 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.825 INFO  Funcotator - Initializing data sources...
13:46:10.825 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.825 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.825 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
13:46:10.825 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
13:46:10.825 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
13:46:10.825 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.826 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
13:46:10.826 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.826 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
13:46:10.826 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
13:46:10.827 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
13:46:10.827 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.827 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
13:46:10.828 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
13:46:10.829 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
13:46:10.830 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.830 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.830 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.
13:46:10.830 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.830 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7315057664598967555.vcf
13:46:10.830 INFO  ProgressMeter - Starting traversal
13:46:10.830 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.860 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
13:46:10.860 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
13:46:10.860 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:10.863 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.931 INFO  Funcotator - ------------------------------------------------------------
13:46:10.931 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:10.931 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:10.931 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:10.931 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:10.931 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:10 PM UTC
13:46:10.931 INFO  Funcotator - ------------------------------------------------------------
13:46:10.931 INFO  Funcotator - ------------------------------------------------------------
13:46:10.931 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:10.931 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:10.931 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:10.931 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:10.931 INFO  Funcotator - Deflater: IntelDeflater
13:46:10.931 INFO  Funcotator - Inflater: IntelInflater
13:46:10.931 INFO  Funcotator - GCS max retries/reopens: 20
13:46:10.931 INFO  Funcotator - Requester pays: disabled
13:46:10.931 INFO  Funcotator - Initializing engine
13:46:10.932 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
13:46:10.932 INFO  Funcotator - Done initializing engine
13:46:10.932 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:10.932 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:10.932 INFO  Funcotator - Initializing data sources...
13:46:10.932 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:10.932 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:10.932 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
13:46:10.933 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
13:46:10.933 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
13:46:10.933 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:10.933 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
13:46:10.933 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:10.933 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
13:46:10.933 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
13:46:10.934 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
13:46:10.934 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:10.934 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
13:46:10.935 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
13:46:10.936 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
13:46:10.937 INFO  Funcotator - Initializing Funcotator Engine...
13:46:10.937 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:10.937 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.
13:46:10.937 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:10.937 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9343599473866532667.maf
13:46:10.937 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
13:46:10.937 INFO  ProgressMeter - Starting traversal
13:46:10.937 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:10.940 WARN  MafOutputRenderer - 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=
13:46:10.940 WARN  MafOutputRenderer - 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=
13:46:10.940 WARN  MafOutputRenderer - 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=
13:46:10.941 WARN  MafOutputRenderer - 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=
13:46:10.942 WARN  MafOutputRenderer - 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=
13:46:10.942 WARN  MafOutputRenderer - 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=
13:46:10.943 WARN  MafOutputRenderer - 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=
13:46:10.943 WARN  MafOutputRenderer - 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=
13:46:10.944 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 @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
13:46:10.944 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 @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
13:46:10.944 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 @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
13:46:10.945 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 @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
13:46:10.945 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 @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
13:46:10.946 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 @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
13:46:10.947 WARN  MafOutputRenderer - 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=
13:46:10.947 WARN  MafOutputRenderer - 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=
13:46:10.948 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 @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
13:46:10.948 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 @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
13:46:10.949 WARN  MafOutputRenderer - 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=
13:46:10.949 WARN  MafOutputRenderer - 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=
13:46:10.950 WARN  MafOutputRenderer - 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=
13:46:10.950 WARN  MafOutputRenderer - 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=
13:46:10.952 WARN  MafOutputRenderer - 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=
13:46:10.952 WARN  MafOutputRenderer - 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=
13:46:10.952 WARN  MafOutputRenderer - 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=
13:46:10.954 WARN  MafOutputRenderer - 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=
13:46:10.954 WARN  MafOutputRenderer - 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=
13:46:10.955 WARN  MafOutputRenderer - 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=
13:46:10.956 WARN  MafOutputRenderer - 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=
13:46:10.956 WARN  MafOutputRenderer - 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=
13:46:10.956 WARN  MafOutputRenderer - 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=
13:46:10.958 WARN  MafOutputRenderer - 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=
13:46:10.958 WARN  MafOutputRenderer - 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=
13:46:10.958 WARN  MafOutputRenderer - 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=
13:46:10.959 WARN  MafOutputRenderer - 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=
13:46:10.960 WARN  MafOutputRenderer - 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=
13:46:10.960 WARN  MafOutputRenderer - 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=
13:46:10.961 WARN  MafOutputRenderer - 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=
13:46:10.962 WARN  MafOutputRenderer - 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=
13:46:10.962 WARN  MafOutputRenderer - 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=
13:46:10.962 WARN  MafOutputRenderer - 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=
13:46:10.964 WARN  MafOutputRenderer - 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=
13:46:10.964 WARN  MafOutputRenderer - 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=
13:46:10.964 WARN  MafOutputRenderer - 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=
13:46:10.965 WARN  MafOutputRenderer - 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=
13:46:10.966 WARN  MafOutputRenderer - 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=
13:46:10.966 WARN  MafOutputRenderer - 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=
13:46:10.967 WARN  MafOutputRenderer - 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=
13:46:10.967 WARN  MafOutputRenderer - 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=
13:46:10.968 WARN  MafOutputRenderer - 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=
13:46:10.969 WARN  MafOutputRenderer - 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=
13:46:10.969 WARN  MafOutputRenderer - 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=
13:46:10.969 WARN  MafOutputRenderer - 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=
13:46:10.971 WARN  MafOutputRenderer - 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=
13:46:10.971 WARN  MafOutputRenderer - 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=
13:46:10.971 WARN  MafOutputRenderer - 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=
13:46:10.972 WARN  MafOutputRenderer - 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=
13:46:10.972 INFO  ProgressMeter -             unmapped              0.0                    57          97714.3
13:46:10.972 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
13:46:10.972 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:10.972 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:10 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2847932416
13:46:10.973 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7315057664598967555.vcf
13:46:11.045 INFO  Funcotator - ------------------------------------------------------------
13:46:11.045 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:11.045 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:11.045 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:11.045 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:11.045 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:11 PM UTC
13:46:11.045 INFO  Funcotator - ------------------------------------------------------------
13:46:11.045 INFO  Funcotator - ------------------------------------------------------------
13:46:11.045 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:11.045 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:11.045 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:11.045 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:11.045 INFO  Funcotator - Deflater: IntelDeflater
13:46:11.045 INFO  Funcotator - Inflater: IntelInflater
13:46:11.045 INFO  Funcotator - GCS max retries/reopens: 20
13:46:11.045 INFO  Funcotator - Requester pays: disabled
13:46:11.045 INFO  Funcotator - Initializing engine
13:46:11.046 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
13:46:11.047 INFO  Funcotator - Done initializing engine
13:46:11.047 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:11.047 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:11.047 INFO  Funcotator - Initializing data sources...
13:46:11.047 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:11.047 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:11.047 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
13:46:11.047 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
13:46:11.047 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
13:46:11.048 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
13:46:11.048 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
13:46:11.048 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
13:46:11.048 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
13:46:11.048 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
13:46:11.048 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
13:46:11.048 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
13:46:11.049 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
13:46:11.049 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
13:46:11.049 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
13:46:11.049 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
13:46:11.049 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:11.049 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:11.049 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
13:46:11.050 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
13:46:11.157 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
13:46:11.187 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
13:46:11.199 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
13:46:11.200 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
13:46:11.200 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
13:46:11.200 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
13:46:11.919 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
13:46:11.956 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
13:46:11.957 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:11.957 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
13:46:11.958 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
13:46:12.046 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:12.046 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:12.047 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
13:46:12.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:12.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:46:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:12.074 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
13:46:12.075 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
13:46:12.075 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
13:46:12.075 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:12.076 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
13:46:12.078 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
13:46:12.081 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
13:46:12.083 INFO  Funcotator - Initializing Funcotator Engine...
13:46:12.083 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:12.083 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:12.083 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17108539280410163703.vcf
13:46:12.084 INFO  ProgressMeter - Starting traversal
13:46:12.084 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:27.754 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7657.9
13:46:28.216 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)
13:46:28.217 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)
13:46:28.956 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7315.1
13:46:28.956 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
13:46:28.956 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
13:46:28.958 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:28 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=3177185280
13:46:29.024 INFO  Funcotator - ------------------------------------------------------------
13:46:29.024 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:29.024 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:29.024 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:29.024 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:29.024 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:29 PM UTC
13:46:29.024 INFO  Funcotator - ------------------------------------------------------------
13:46:29.024 INFO  Funcotator - ------------------------------------------------------------
13:46:29.024 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:29.024 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:29.024 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:29.024 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:29.024 INFO  Funcotator - Deflater: IntelDeflater
13:46:29.024 INFO  Funcotator - Inflater: IntelInflater
13:46:29.024 INFO  Funcotator - GCS max retries/reopens: 20
13:46:29.024 INFO  Funcotator - Requester pays: disabled
13:46:29.024 INFO  Funcotator - Initializing engine
13:46:29.025 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
13:46:29.025 INFO  Funcotator - Done initializing engine
13:46:29.025 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:29.025 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:29.025 INFO  Funcotator - Initializing data sources...
13:46:29.025 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
13:46:29.025 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:29.025 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
13:46:29.026 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
13:46:29.026 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
13:46:29.026 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
13:46:29.026 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
13:46:29.026 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
13:46:29.026 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
13:46:29.026 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
13:46:29.027 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
13:46:29.027 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
13:46:29.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
13:46:29.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:29.027 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
13:46:29.027 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
13:46:29.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:29.027 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:29.027 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
13:46:29.028 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
13:46:29.070 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
13:46:29.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
13:46:29.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
13:46:29.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
13:46:29.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
13:46:29.095 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
13:46:29.668 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
13:46:29.706 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
13:46:29.706 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:29.707 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
13:46:29.707 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
13:46:29.791 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:29.791 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:29.792 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
13:46:29.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
13:46:29.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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 13:46:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:29.819 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
13:46:29.819 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
13:46:29.820 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:29.820 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
13:46:29.820 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
13:46:29.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
13:46:29.825 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
13:46:29.827 INFO  Funcotator - Initializing Funcotator Engine...
13:46:29.827 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:29.827 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:29.827 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4825470517253326462.maf
13:46:29.827 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
13:46:29.827 INFO  ProgressMeter - Starting traversal
13:46:29.827 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:45.479 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7666.8
13:46:45.943 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)
13:46:45.945 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)
13:46:46.672 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7326.8
13:46:46.672 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
13:46:46.672 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
13:46:46.673 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:46 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=3177185280
13:46:46.674 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17108539280410163703.vcf
13:46:47.046 INFO  Funcotator - ------------------------------------------------------------
13:46:47.046 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.046 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.046 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.046 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.046 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.046 INFO  Funcotator - ------------------------------------------------------------
13:46:47.046 INFO  Funcotator - ------------------------------------------------------------
13:46:47.046 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.046 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.046 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.046 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.046 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.046 INFO  Funcotator - Inflater: IntelInflater
13:46:47.046 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.046 INFO  Funcotator - Requester pays: disabled
13:46:47.046 INFO  Funcotator - Initializing engine
13:46:47.047 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
13:46:47.062 INFO  Funcotator - Done initializing engine
13:46:47.062 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.062 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.062 INFO  Funcotator - Initializing data sources...
13:46:47.062 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:47.062 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.063 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
13:46:47.063 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
13:46:47.063 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
13:46:47.063 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.063 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
13:46:47.063 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.064 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
13:46:47.064 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
13:46:47.064 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
13:46:47.064 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:47.065 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
13:46:47.072 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
13:46:47.081 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
13:46:47.088 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.093 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:47.093 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3172393219967397874.vcf
13:46:47.105 INFO  ProgressMeter - Starting traversal
13:46:47.105 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.127 INFO  ProgressMeter -             unmapped              0.0                   100         272727.3
13:46:47.127 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
13:46:47.127 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:47.132 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.196 INFO  Funcotator - ------------------------------------------------------------
13:46:47.196 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.196 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.196 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.196 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.196 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.196 INFO  Funcotator - ------------------------------------------------------------
13:46:47.196 INFO  Funcotator - ------------------------------------------------------------
13:46:47.196 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.196 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.196 INFO  Funcotator - Inflater: IntelInflater
13:46:47.196 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.196 INFO  Funcotator - Requester pays: disabled
13:46:47.197 INFO  Funcotator - Initializing engine
13:46:47.197 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
13:46:47.213 INFO  Funcotator - Done initializing engine
13:46:47.213 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.213 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.213 INFO  Funcotator - Initializing data sources...
13:46:47.213 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:47.213 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.213 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
13:46:47.213 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
13:46:47.214 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
13:46:47.214 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.214 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
13:46:47.214 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.214 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
13:46:47.214 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
13:46:47.215 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
13:46:47.215 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:47.215 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
13:46:47.223 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
13:46:47.232 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
13:46:47.240 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.244 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:47.244 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1337429855907636982.maf
13:46:47.245 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
13:46:47.245 INFO  ProgressMeter - Starting traversal
13:46:47.245 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.248 WARN  MafOutputRenderer - 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=
13:46:47.252 WARN  MafOutputRenderer - 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=
13:46:47.253 WARN  MafOutputRenderer - 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+
13:46:47.253 WARN  MafOutputRenderer - 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+
13:46:47.253 WARN  MafOutputRenderer - 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+
13:46:47.253 WARN  MafOutputRenderer - 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+
13:46:47.254 WARN  MafOutputRenderer - 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=
13:46:47.254 WARN  MafOutputRenderer - 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=
13:46:47.254 WARN  MafOutputRenderer - 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=
13:46:47.255 WARN  MafOutputRenderer - 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=
13:46:47.255 WARN  MafOutputRenderer - 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=
13:46:47.255 WARN  MafOutputRenderer - 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=
13:46:47.255 WARN  MafOutputRenderer - 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=
13:46:47.256 WARN  MafOutputRenderer - 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=
13:46:47.256 WARN  MafOutputRenderer - 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=
13:46:47.256 WARN  MafOutputRenderer - 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=
13:46:47.256 WARN  MafOutputRenderer - 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=
13:46:47.257 WARN  MafOutputRenderer - 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=
13:46:47.257 WARN  MafOutputRenderer - 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=
13:46:47.257 WARN  MafOutputRenderer - 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+
13:46:47.257 WARN  MafOutputRenderer - 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
13:46:47.258 WARN  MafOutputRenderer - 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=
13:46:47.258 WARN  MafOutputRenderer - 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=
13:46:47.258 WARN  MafOutputRenderer - 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=
13:46:47.258 WARN  MafOutputRenderer - 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=
13:46:47.259 WARN  MafOutputRenderer - 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=
13:46:47.259 WARN  MafOutputRenderer - 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=
13:46:47.259 WARN  MafOutputRenderer - 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=
13:46:47.259 WARN  MafOutputRenderer - 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
13:46:47.259 WARN  MafOutputRenderer - 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=
13:46:47.260 WARN  MafOutputRenderer - 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=
13:46:47.260 WARN  MafOutputRenderer - 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=
13:46:47.260 WARN  MafOutputRenderer - 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=
13:46:47.260 WARN  MafOutputRenderer - 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=
13:46:47.260 WARN  MafOutputRenderer - 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=
13:46:47.261 WARN  MafOutputRenderer - 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=
13:46:47.261 WARN  MafOutputRenderer - 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=
13:46:47.261 WARN  MafOutputRenderer - 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=
13:46:47.261 WARN  MafOutputRenderer - 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=
13:46:47.261 WARN  MafOutputRenderer - 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=
13:46:47.262 WARN  MafOutputRenderer - 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=
13:46:47.263 WARN  MafOutputRenderer - 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=
13:46:47.263 WARN  MafOutputRenderer - 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=
13:46:47.263 WARN  MafOutputRenderer - 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=
13:46:47.263 WARN  MafOutputRenderer - 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=
13:46:47.264 WARN  MafOutputRenderer - 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=
13:46:47.264 WARN  MafOutputRenderer - 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+
13:46:47.264 WARN  MafOutputRenderer - 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=
13:46:47.264 WARN  MafOutputRenderer - 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=
13:46:47.264 WARN  MafOutputRenderer - 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=
13:46:47.264 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.265 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.266 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.267 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.268 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.269 WARN  MafOutputRenderer - 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=
13:46:47.270 WARN  MafOutputRenderer - 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=
13:46:47.270 WARN  MafOutputRenderer - 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=
13:46:47.270 WARN  MafOutputRenderer - 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=
13:46:47.270 WARN  MafOutputRenderer - 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=
13:46:47.270 WARN  MafOutputRenderer - 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=
13:46:47.271 WARN  MafOutputRenderer - 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=
13:46:47.271 WARN  MafOutputRenderer - 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=
13:46:47.271 WARN  MafOutputRenderer - 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=
13:46:47.271 WARN  MafOutputRenderer - 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=
13:46:47.272 WARN  MafOutputRenderer - 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=
13:46:47.272 WARN  MafOutputRenderer - 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=
13:46:47.272 WARN  MafOutputRenderer - 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=
13:46:47.273 WARN  MafOutputRenderer - 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=
13:46:47.273 WARN  MafOutputRenderer - 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=
13:46:47.273 WARN  MafOutputRenderer - 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=
13:46:47.273 WARN  MafOutputRenderer - 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=
13:46:47.273 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
13:46:47.273 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
13:46:47.273 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:47.274 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.275 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3172393219967397874.vcf
13:46:47.407 INFO  Funcotator - ------------------------------------------------------------
13:46:47.407 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.407 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.407 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.407 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.407 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.407 INFO  Funcotator - ------------------------------------------------------------
13:46:47.407 INFO  Funcotator - ------------------------------------------------------------
13:46:47.408 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.408 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.408 INFO  Funcotator - Inflater: IntelInflater
13:46:47.408 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.408 INFO  Funcotator - Requester pays: disabled
13:46:47.408 INFO  Funcotator - Initializing engine
13:46:47.409 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
13:46:47.409 INFO  Funcotator - Done initializing engine
13:46:47.409 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.409 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.409 INFO  Funcotator - Initializing data sources...
13:46:47.409 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:47.409 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.409 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
13:46:47.409 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
13:46:47.409 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
13:46:47.409 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.409 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
13:46:47.409 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.410 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
13:46:47.410 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
13:46:47.411 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
13:46:47.411 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:47.411 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
13:46:47.412 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
13:46:47.413 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
13:46:47.413 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.413 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:47.413 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.
13:46:47.413 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:47.413 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8077681763764919129.vcf
13:46:47.414 INFO  ProgressMeter - Starting traversal
13:46:47.414 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.443 INFO  ProgressMeter -             unmapped              0.0                    57         117931.0
13:46:47.443 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
13:46:47.443 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:47.445 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.513 INFO  Funcotator - ------------------------------------------------------------
13:46:47.513 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.513 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.513 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.513 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.513 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.513 INFO  Funcotator - ------------------------------------------------------------
13:46:47.513 INFO  Funcotator - ------------------------------------------------------------
13:46:47.513 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.513 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.513 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.513 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.513 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.513 INFO  Funcotator - Inflater: IntelInflater
13:46:47.513 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.513 INFO  Funcotator - Requester pays: disabled
13:46:47.513 INFO  Funcotator - Initializing engine
13:46:47.514 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
13:46:47.514 INFO  Funcotator - Done initializing engine
13:46:47.514 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.514 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.514 INFO  Funcotator - Initializing data sources...
13:46:47.514 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:47.514 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.514 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
13:46:47.514 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
13:46:47.514 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
13:46:47.514 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.515 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
13:46:47.515 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.515 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
13:46:47.515 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
13:46:47.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:47.516 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:47.516 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
13:46:47.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:47.518 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
13:46:47.518 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.518 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:47.518 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.
13:46:47.518 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
13:46:47.518 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3693904255860087322.maf
13:46:47.519 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
13:46:47.519 INFO  ProgressMeter - Starting traversal
13:46:47.519 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.521 WARN  MafOutputRenderer - 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=
13:46:47.522 WARN  MafOutputRenderer - 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=
13:46:47.522 WARN  MafOutputRenderer - 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=
13:46:47.522 WARN  MafOutputRenderer - 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=
13:46:47.523 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
13:46:47.524 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
13:46:47.524 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
13:46:47.525 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
13:46:47.525 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
13:46:47.526 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
13:46:47.526 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
13:46:47.527 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
13:46:47.527 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
13:46:47.530 WARN  MafOutputRenderer - 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=
13:46:47.530 WARN  MafOutputRenderer - 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=
13:46:47.531 WARN  MafOutputRenderer - 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=
13:46:47.532 WARN  MafOutputRenderer - 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=
13:46:47.532 WARN  MafOutputRenderer - 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=
13:46:47.533 WARN  MafOutputRenderer - 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=
13:46:47.533 WARN  MafOutputRenderer - 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=
13:46:47.535 WARN  MafOutputRenderer - 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=
13:46:47.535 WARN  MafOutputRenderer - 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=
13:46:47.537 WARN  MafOutputRenderer - 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=
13:46:47.538 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
13:46:47.538 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
13:46:47.540 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
13:46:47.541 WARN  MafOutputRenderer - 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=
13:46:47.543 WARN  MafOutputRenderer - 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=
13:46:47.543 WARN  MafOutputRenderer - 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=
13:46:47.544 WARN  MafOutputRenderer - 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=
13:46:47.544 WARN  MafOutputRenderer - 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=
13:46:47.546 WARN  MafOutputRenderer - 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=
13:46:47.547 WARN  MafOutputRenderer - 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=
13:46:47.547 WARN  MafOutputRenderer - 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=
13:46:47.548 WARN  MafOutputRenderer - 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=
13:46:47.549 WARN  MafOutputRenderer - 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=
13:46:47.550 WARN  MafOutputRenderer - 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=
13:46:47.552 WARN  MafOutputRenderer - 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=
13:46:47.552 WARN  MafOutputRenderer - 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=
13:46:47.553 WARN  MafOutputRenderer - 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=
13:46:47.553 WARN  MafOutputRenderer - 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=
13:46:47.554 WARN  MafOutputRenderer - 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=
13:46:47.555 WARN  MafOutputRenderer - 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=
13:46:47.555 WARN  MafOutputRenderer - 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=
13:46:47.555 WARN  MafOutputRenderer - 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=
13:46:47.557 WARN  MafOutputRenderer - 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=
13:46:47.557 WARN  MafOutputRenderer - 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=
13:46:47.557 WARN  MafOutputRenderer - 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=
13:46:47.558 WARN  MafOutputRenderer - 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=
13:46:47.559 WARN  MafOutputRenderer - 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=
13:46:47.559 WARN  MafOutputRenderer - 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=
13:46:47.560 WARN  MafOutputRenderer - 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=
13:46:47.560 WARN  MafOutputRenderer - 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=
13:46:47.561 WARN  MafOutputRenderer - 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=
13:46:47.561 WARN  MafOutputRenderer - 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=
13:46:47.562 WARN  MafOutputRenderer - 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=
13:46:47.562 WARN  MafOutputRenderer - 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=
13:46:47.562 INFO  ProgressMeter -             unmapped              0.0                    57          79534.9
13:46:47.562 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
13:46:47.562 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
13:46:47.562 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.563 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8077681763764919129.vcf
13:46:47.660 INFO  Funcotator - ------------------------------------------------------------
13:46:47.660 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.660 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.660 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.660 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.660 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.660 INFO  Funcotator - ------------------------------------------------------------
13:46:47.660 INFO  Funcotator - ------------------------------------------------------------
13:46:47.660 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.660 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.660 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.660 INFO  Funcotator - Inflater: IntelInflater
13:46:47.660 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.660 INFO  Funcotator - Requester pays: disabled
13:46:47.660 INFO  Funcotator - Initializing engine
13:46:47.661 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
13:46:47.662 INFO  Funcotator - Done initializing engine
13:46:47.662 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.662 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.662 INFO  Funcotator - Initializing data sources...
13:46:47.662 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
13:46:47.662 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.663 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
13:46:47.663 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
13:46:47.663 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
13:46:47.663 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.663 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
13:46:47.663 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.664 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
13:46:47.664 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
13:46:47.664 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
13:46:47.664 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
13:46:47.665 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
13:46:47.665 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
13:46:47.666 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
13:46:47.667 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.667 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:47.667 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.
13:46:47.667 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3588142661705520274.maf
13:46:47.668 INFO  ProgressMeter - Starting traversal
13:46:47.668 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.670 WARN  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=
13:46:47.671 WARN  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=
13:46:47.671 WARN  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=
13:46:47.672 WARN  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=
13:46:47.672 WARN  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=
13:46:47.673 WARN  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=
13:46:47.673 WARN  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=
13:46:47.674 WARN  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=
13:46:47.674 WARN  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=
13:46:47.674 WARN  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=
13:46:47.675 WARN  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=
13:46:47.675 WARN  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=
13:46:47.675 WARN  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=
13:46:47.676 WARN  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=
13:46:47.676 WARN  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=
13:46:47.676 WARN  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=
13:46:47.676 WARN  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=
13:46:47.677 WARN  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=
13:46:47.677 WARN  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=
13:46:47.677 WARN  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=
13:46:47.677 WARN  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=
13:46:47.677 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
13:46:47.677 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
13:46:47.677 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
13:46:47.678 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.750 INFO  Funcotator - ------------------------------------------------------------
13:46:47.750 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.750 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.750 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.750 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.750 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.750 INFO  Funcotator - ------------------------------------------------------------
13:46:47.750 INFO  Funcotator - ------------------------------------------------------------
13:46:47.750 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.750 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.750 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.750 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.750 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.750 INFO  Funcotator - Inflater: IntelInflater
13:46:47.750 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.750 INFO  Funcotator - Requester pays: disabled
13:46:47.750 INFO  Funcotator - Initializing engine
13:46:47.751 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
13:46:47.752 INFO  Funcotator - Done initializing engine
13:46:47.752 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.752 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.752 INFO  Funcotator - Initializing data sources...
13:46:47.752 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
13:46:47.752 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.752 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
13:46:47.752 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
13:46:47.752 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
13:46:47.752 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.752 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:47.753 INFO  DataSourceUtils - Resolved 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
13:46:47.753 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
13:46:47.781 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
13:46:47.781 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 13:46:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:47.781 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
13:46:47.781 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.782 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
13:46:47.782 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
13:46:47.782 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.783 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:47.783 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.
13:46:47.783 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4085365551156946992.vcf
13:46:47.786 INFO  ProgressMeter - Starting traversal
13:46:47.786 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.790 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
13:46:47.790 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
13:46:47.790 WARN  Funcotator - ================================================================================
13:46:47.790 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:47.790 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:47.790 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:47.790 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:47.790 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:47.790 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:47.790 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:47.790 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:47.790 WARN  Funcotator -  run was misconfigured.     
13:46:47.790 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:47.790 WARN  Funcotator - ================================================================================
13:46:47.790 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.791 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4085365551156946992.vcf
13:46:47.860 INFO  Funcotator - ------------------------------------------------------------
13:46:47.860 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
13:46:47.860 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:47.860 INFO  Funcotator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:46:47.860 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:46:47.860 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:46:47 PM UTC
13:46:47.860 INFO  Funcotator - ------------------------------------------------------------
13:46:47.860 INFO  Funcotator - ------------------------------------------------------------
13:46:47.860 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:47.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:47.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:47.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:47.860 INFO  Funcotator - Deflater: IntelDeflater
13:46:47.860 INFO  Funcotator - Inflater: IntelInflater
13:46:47.860 INFO  Funcotator - GCS max retries/reopens: 20
13:46:47.860 INFO  Funcotator - Requester pays: disabled
13:46:47.860 INFO  Funcotator - Initializing engine
13:46:47.861 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
13:46:47.862 INFO  Funcotator - Done initializing engine
13:46:47.862 INFO  Funcotator - Skipping sequence dictionary validation.
13:46:47.862 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:47.862 INFO  Funcotator - Initializing data sources...
13:46:47.862 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
13:46:47.862 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:46:47.862 INFO  DataSourceUtils - Resolved 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
13:46:47.862 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
13:46:47.862 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
13:46:47.862 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:47.862 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
13:46:47.863 INFO  DataSourceUtils - Resolved 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
13:46:47.863 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
13:46:47.891 INFO  DataSourceUtils - Resolved 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
13:46:47.891 INFO  DataSourceUtils - Resolved 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 13:46:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
13:46:47.891 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
13:46:47.891 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:47.892 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
13:46:47.892 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
13:46:47.893 INFO  Funcotator - Initializing Funcotator Engine...
13:46:47.893 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
13:46:47.893 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.
13:46:47.893 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17140147043752474609.vcf
13:46:47.896 INFO  ProgressMeter - Starting traversal
13:46:47.896 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:47.898 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
13:46:47.898 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
13:46:47.898 WARN  Funcotator - ================================================================================
13:46:47.898 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
13:46:47.898 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
13:46:47.898 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
13:46:47.898 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
13:46:47.898 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
13:46:47.898 WARN  Funcotator -                                                   |___/                         ?[0;0m
13:46:47.898 WARN  Funcotator - --------------------------------------------------------------------------------
13:46:47.898 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
13:46:47.898 WARN  Funcotator -  run was misconfigured.     
13:46:47.898 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
13:46:47.898 WARN  Funcotator - ================================================================================
13:46:47.899 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 1:46:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
13:46:47.899 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17140147043752474609.vcf