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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
tests
failures
ignored
1m57.71s
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/funcotatorTmpFolder6071080130541696521/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null)	0.660s	passed
exhaustiveArgumentTest[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.646s	passed
exhaustiveArgumentTest[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.502s	passed
exhaustiveArgumentTest[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.619s	passed
exhaustiveArgumentTest[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.513s	passed
exhaustiveArgumentTest[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null)	0.608s	passed
exhaustiveArgumentTest[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.476s	passed
exhaustiveArgumentTest[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.596s	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)	7.404s	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)	6.569s	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)	0.913s	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)	0.911s	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)	15.807s	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)	7.310s	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)	0.066s	passed
testCanAnnotateHg38ClinvarAndGencodeV28	0.179s	passed
testCanAnnotateMixedContigHg19Clinvar	0.091s	passed
testCanAnnotateSpanningDeletions	0.161s	passed
testCanCreateNonLocatableFuncotations	0.515s	passed
testCanHandleSymbollicAlleleFuncotations	0.555s	passed
testCustomVariantClassificationOrder	0.487s	passed
testEColiFuncotations	0.099s	passed
testEnsureDbSnpInMaf	0.075s	passed
testExclusionFromDatasourceVcfToVcf	0.179s	passed
testFilterParsing	0.123s	passed
testFuncotatorWithoutValidatingResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/GRCh37.p13.chr3.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null)	0.475s	passed
testFuncotatorWithoutValidatingResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.664s	passed
testFuncotatorWithoutValidatingResults[2](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.461s	passed
testFuncotatorWithoutValidatingResults[3](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.622s	passed
testFuncotatorWithoutValidatingResults[4](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.487s	passed
testFuncotatorWithoutValidatingResults[5](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/GRCh37.p13.chr19.fasta, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null)	0.640s	passed
testFuncotatorWithoutValidatingResults[6](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder6071080130541696521/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)	0.495s	passed
testFuncotatorWithoutValidatingResults[7](/home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3657071588561573748/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)	0.644s	passed
testMANESelectAnnotationDifferencesAndGencodeV43	0.323s	passed
testMafCustomCountFieldsTumorOnly[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf)	0.080s	passed
testMafCustomCountFieldsTumorOnly[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf)	0.077s	passed
testMafCustomCountFields[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf)	0.080s	passed
testMafCustomCountFields[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf)	0.079s	passed
testManualAnnotationsCorrectness	0.119s	passed
testMoreThanOneTNPair	0.072s	passed
testNoSpanningDeletionWriteWithMAF	0.130s	passed
testNoVariantsProduceMaf	0.071s	passed
testSequenceDictionaryCheck	0.065s	passed
testUnannotatedInputWithOverrideArgument[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf)	7.214s	passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput	0.390s	passed
testVCFColumnsArentShuffled	0.081s	passed
testVCFToMAFPreservesFields	0.089s	passed
testVCFToVCFPreservesFields	0.089s	passed
testVcfDatasourceAccountsForAltAlleles	0.079s	passed
testVcfMafConcordance[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder16609871356989887736/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15)	0.164s	passed
testVcfMafConcordance[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder16609871356989887736/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.222s	passed
testVcfMafConcordance[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder3657071588561573748/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057)	56.768s	passed
testVcfMafConcordance[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder8301568103397181047/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)	0.394s	passed
testVcfMafConcordance[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder16609871356989887736/b37.3.fasta, hg19, [Gencode_19_hugoSymbol, Gencode_19_ncbiBuild, Gencode_19_chromosome, Gencode_19_start, Gencode_19_end, Gencode_19_variantClassification, Gencode_19_variantType, Gencode_19_refAllele, Gencode_19_tumorSeqAllele1, Gencode_19_tumorSeqAllele2, Gencode_19_genomeChange, Gencode_19_annotationTranscript, Gencode_19_transcriptStrand, Gencode_19_transcriptExon, Gencode_19_transcriptPos, Gencode_19_cDnaChange, Gencode_19_codonChange, Gencode_19_proteinChange, Gencode_19_gcContent, Gencode_19_referenceContext, Gencode_19_otherTranscripts], [Hugo_Symbol, NCBI_Build, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Genome_Change, Annotation_Transcript, Transcript_Strand, Transcript_Exon, Transcript_Position, cDNA_Change, Codon_Change, Protein_Change, gc_content, ref_context, Other_Transcripts], /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57)	0.248s	passed
testVcfToMafHonorsExcludedFields	0.085s	passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified	0.120s	passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations	0.118s	passed
Standard error

17:42:59.389 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:42:59.392 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14890130808324768076.so: /tmp/libgkl_compression14890130808324768076.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:42:59.392 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:42:59.395 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11423283209909555379.so: /tmp/libgkl_compression11423283209909555379.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:42:59.396 INFO  Funcotator - ------------------------------------------------------------
17:42:59.396 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:42:59.396 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:42:59.396 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:42:59.396 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:42:59.396 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:42:59 PM UTC
17:42:59.396 INFO  Funcotator - ------------------------------------------------------------
17:42:59.396 INFO  Funcotator - ------------------------------------------------------------
17:42:59.396 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:42:59.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:42:59.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:42:59.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:42:59.396 INFO  Funcotator - Deflater: JdkDeflater
17:42:59.396 INFO  Funcotator - Inflater: JdkInflater
17:42:59.396 INFO  Funcotator - GCS max retries/reopens: 20
17:42:59.397 INFO  Funcotator - Requester pays: disabled
17:42:59.397 INFO  Funcotator - Initializing engine
17:42:59.398 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
17:42:59.399 INFO  Funcotator - Done initializing engine
17:42:59.399 INFO  Funcotator - Skipping sequence dictionary validation.
17:42:59.399 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:42:59.399 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8774198549536578888/TranscriptIdFile.txt
17:42:59.399 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
17:42:59.399 INFO  FuncotatorEngine - Transcript parsing complete.
17:42:59.400 INFO  Funcotator - Initializing data sources...
17:42:59.400 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:42:59.400 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:42:59.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:42:59.400 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:42:59.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:42:59.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:42:59.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:42:59.401 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:42:59.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:42:59.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:42:59.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:42:59.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:42:59.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:42:59.403 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:42:59.403 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:42:59.403 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:42:59.403 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:42:59.403 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:42:59.403 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:42:59.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:42:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:42:59.575 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
17:42:59.582 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
17:42:59.582 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
17:42:59.582 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
17:42:59.583 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:42:59.583 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:42:59.584 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
17:42:59.584 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:42:59.672 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:42:59.684 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:42:59.865 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:42:59.865 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:42:59.866 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
17:42:59.906 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:42:59.906 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:42:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:42:59.907 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:42:59.908 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:42:59.908 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:42:59.908 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:42:59.908 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.909 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:42:59.909 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.909 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.911 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.912 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:42:59.912 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.912 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.913 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.914 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.915 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:42:59.915 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.915 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.917 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:59.918 INFO  Funcotator - Initializing Funcotator Engine...
17:42:59.918 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
17:42:59.918 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:42:59.918 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:42:59.919 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:42:59.919 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:42:59.920 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:42:59.920 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:42:59.920 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.314626185863102628870.vcf
17:42:59.921 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
17:42:59.924 INFO  ProgressMeter - Starting traversal
17:42:59.924 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:42:59.991 INFO  ProgressMeter -             unmapped              0.0                     3           2686.6
17:42:59.991 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:42:59.992 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:42:59.994 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:42:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:00.052 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:00.055 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8299231613293687124.so: /tmp/libgkl_compression8299231613293687124.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:00.055 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:00.058 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression458825959492907353.so: /tmp/libgkl_compression458825959492907353.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:00.059 INFO  Funcotator - ------------------------------------------------------------
17:43:00.059 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:00.059 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:00.059 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:00.059 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:00.059 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:00 PM UTC
17:43:00.059 INFO  Funcotator - ------------------------------------------------------------
17:43:00.059 INFO  Funcotator - ------------------------------------------------------------
17:43:00.059 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:00.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:00.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:00.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:00.059 INFO  Funcotator - Deflater: JdkDeflater
17:43:00.059 INFO  Funcotator - Inflater: JdkInflater
17:43:00.059 INFO  Funcotator - GCS max retries/reopens: 20
17:43:00.059 INFO  Funcotator - Requester pays: disabled
17:43:00.059 INFO  Funcotator - Initializing engine
17:43:00.061 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
17:43:00.061 INFO  Funcotator - Done initializing engine
17:43:00.061 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:00.061 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:00.061 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder7488514526523129914/TranscriptIdFile.txt
17:43:00.061 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
17:43:00.062 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:00.062 INFO  Funcotator - Initializing data sources...
17:43:00.062 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:00.062 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:00.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:00.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:00.062 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:00.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:00.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:00.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:00.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:00.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:00.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:00.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.065 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:00.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:00.111 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:00.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:00.134 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:00.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:00.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:00.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:00.142 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:00.142 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:00.143 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
17:43:00.143 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:00.223 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:00.236 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:00.375 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:00.376 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:00.377 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
17:43:00.416 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:00.416 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:00.417 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:00.417 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:00.418 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.418 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:00.418 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.419 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.419 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.420 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.421 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.422 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.422 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.423 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.424 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.425 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.425 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.425 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.426 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:00.427 INFO  Funcotator - Initializing Funcotator Engine...
17:43:00.428 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:00.428 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:00.428 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.44245345682405888190.vcf
17:43:00.429 INFO  ProgressMeter - Starting traversal
17:43:00.429 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:00.640 INFO  ProgressMeter -             unmapped              0.0                     4           1137.4
17:43:00.640 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:00.640 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:00.640 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:00 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:00.697 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:00.699 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10188968302505944418.so: /tmp/libgkl_compression10188968302505944418.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:00.700 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:00.702 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13488099266514380026.so: /tmp/libgkl_compression13488099266514380026.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:00.703 INFO  Funcotator - ------------------------------------------------------------
17:43:00.703 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:00.703 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:00.703 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:00.703 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:00.704 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:00 PM UTC
17:43:00.704 INFO  Funcotator - ------------------------------------------------------------
17:43:00.704 INFO  Funcotator - ------------------------------------------------------------
17:43:00.704 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:00.704 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:00.704 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:00.704 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:00.704 INFO  Funcotator - Deflater: JdkDeflater
17:43:00.704 INFO  Funcotator - Inflater: JdkInflater
17:43:00.704 INFO  Funcotator - GCS max retries/reopens: 20
17:43:00.704 INFO  Funcotator - Requester pays: disabled
17:43:00.704 INFO  Funcotator - Initializing engine
17:43:00.705 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
17:43:00.706 INFO  Funcotator - Done initializing engine
17:43:00.706 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:00.706 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:00.706 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder10170606938199154629/TranscriptIdFile.txt
17:43:00.706 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
17:43:00.706 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:00.706 INFO  Funcotator - Initializing data sources...
17:43:00.706 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:00.706 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:00.706 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:00.706 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:00.707 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:00.707 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:00.707 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:00.707 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:00.707 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:00.708 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
17:43:00.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:00.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:00.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:00.708 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:00.709 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:00.709 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:00.709 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:00.709 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:00.709 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:00.755 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:00.756 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:00.777 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:00.784 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:00.785 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:00.785 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:00.785 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:00.785 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:00.786 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
17:43:00.787 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:00.866 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:00.879 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:01.048 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:01.048 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:01.049 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
17:43:01.087 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:01.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:01.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:01.089 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:01.089 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.089 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:01.089 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.090 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.090 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.090 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.091 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.093 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.093 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.093 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.094 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.095 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.096 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.096 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.096 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.097 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.098 INFO  Funcotator - Initializing Funcotator Engine...
17:43:01.098 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
17:43:01.099 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:01.099 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:01.099 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:01.099 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:01.100 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:01.100 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:01.100 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.310590971249915522133.vcf
17:43:01.100 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
17:43:01.101 INFO  ProgressMeter - Starting traversal
17:43:01.101 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:01.139 INFO  ProgressMeter -             unmapped              0.0                     3           4736.8
17:43:01.140 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:01.140 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:01.143 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:01.200 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:01.203 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6578173753778321937.so: /tmp/libgkl_compression6578173753778321937.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:01.203 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:01.206 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8705311103569199352.so: /tmp/libgkl_compression8705311103569199352.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:01.207 INFO  Funcotator - ------------------------------------------------------------
17:43:01.207 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:01.207 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:01.207 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:01.207 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:01.207 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:01 PM UTC
17:43:01.207 INFO  Funcotator - ------------------------------------------------------------
17:43:01.207 INFO  Funcotator - ------------------------------------------------------------
17:43:01.207 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:01.207 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:01.207 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:01.207 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:01.207 INFO  Funcotator - Deflater: JdkDeflater
17:43:01.207 INFO  Funcotator - Inflater: JdkInflater
17:43:01.207 INFO  Funcotator - GCS max retries/reopens: 20
17:43:01.207 INFO  Funcotator - Requester pays: disabled
17:43:01.207 INFO  Funcotator - Initializing engine
17:43:01.208 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
17:43:01.209 INFO  Funcotator - Done initializing engine
17:43:01.209 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:01.209 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:01.209 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder11578274239740149485/TranscriptIdFile.txt
17:43:01.209 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
17:43:01.209 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:01.209 INFO  Funcotator - Initializing data sources...
17:43:01.209 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:01.209 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:01.210 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:01.210 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:01.210 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:01.211 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:01.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:01.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:01.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:01.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:01.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:01.213 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.213 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:01.213 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:01.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:01.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:01.281 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:01.288 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:01.289 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:01.289 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:01.289 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:01.290 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:01.290 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
17:43:01.291 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:01.369 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
17:43:01.382 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:01.521 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:01.522 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
17:43:01.522 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
17:43:01.562 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:01.562 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:01.563 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:01.563 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:01.563 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.563 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:01.564 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.564 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.565 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.565 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.566 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.567 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.567 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.567 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.568 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.569 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.570 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:01.570 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.570 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.572 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:01.573 INFO  Funcotator - Initializing Funcotator Engine...
17:43:01.573 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:01.573 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:01.573 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.4412470105901419214.vcf
17:43:01.574 INFO  ProgressMeter - Starting traversal
17:43:01.574 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:01.760 INFO  ProgressMeter -             unmapped              0.0                     4           1290.3
17:43:01.761 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:01.761 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:01.761 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:01 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:01.819 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:01.822 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7291034591820255571.so: /tmp/libgkl_compression7291034591820255571.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:01.822 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:01.825 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17399291539822499841.so: /tmp/libgkl_compression17399291539822499841.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:01.826 INFO  Funcotator - ------------------------------------------------------------
17:43:01.826 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:01.826 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:01.826 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:01.826 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:01.826 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:01 PM UTC
17:43:01.826 INFO  Funcotator - ------------------------------------------------------------
17:43:01.826 INFO  Funcotator - ------------------------------------------------------------
17:43:01.826 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:01.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:01.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:01.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:01.826 INFO  Funcotator - Deflater: JdkDeflater
17:43:01.826 INFO  Funcotator - Inflater: JdkInflater
17:43:01.826 INFO  Funcotator - GCS max retries/reopens: 20
17:43:01.826 INFO  Funcotator - Requester pays: disabled
17:43:01.826 INFO  Funcotator - Initializing engine
17:43:01.827 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
17:43:01.828 INFO  Funcotator - Done initializing engine
17:43:01.828 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:01.828 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:01.828 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder3241661921383706050/TranscriptIdFile.txt
17:43:01.828 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
17:43:01.828 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:01.828 INFO  Funcotator - Initializing data sources...
17:43:01.828 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:01.828 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:01.828 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
17:43:01.829 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:01.829 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:01.829 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
17:43:01.829 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
17:43:01.829 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
17:43:01.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:01.830 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
17:43:01.830 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
17:43:01.830 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
17:43:01.830 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:01.830 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
17:43:01.830 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
17:43:01.831 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:01.831 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
17:43:01.831 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:01.831 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
17:43:01.877 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:01.878 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:01.900 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:01.907 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:01.907 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:01.908 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:01.908 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:01.908 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:01.909 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
17:43:01.910 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:01.987 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:02.039 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:02.178 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:02.179 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.179 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
17:43:02.219 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.219 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:02.219 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:02.220 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:02.220 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.220 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:02.220 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.221 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.221 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.221 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.223 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.224 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.224 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.224 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.225 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.226 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.227 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.227 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.227 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.228 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.229 INFO  Funcotator - Initializing Funcotator Engine...
17:43:02.229 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
17:43:02.230 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:02.230 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:02.230 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:02.230 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:02.231 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:02.231 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:02.231 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.37356599783798527924.maf
17:43:02.234 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
17:43:02.235 INFO  ProgressMeter - Starting traversal
17:43:02.235 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:02.274 INFO  ProgressMeter -             unmapped              0.0                     3           4615.4
17:43:02.275 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:02.275 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:02.275 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:02.331 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:02.334 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6620989346632225508.so: /tmp/libgkl_compression6620989346632225508.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:02.334 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:02.337 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9095760438947948549.so: /tmp/libgkl_compression9095760438947948549.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:02.338 INFO  Funcotator - ------------------------------------------------------------
17:43:02.338 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:02.338 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:02.338 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:02.338 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:02.338 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:02 PM UTC
17:43:02.338 INFO  Funcotator - ------------------------------------------------------------
17:43:02.338 INFO  Funcotator - ------------------------------------------------------------
17:43:02.339 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:02.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:02.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:02.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:02.339 INFO  Funcotator - Deflater: JdkDeflater
17:43:02.339 INFO  Funcotator - Inflater: JdkInflater
17:43:02.339 INFO  Funcotator - GCS max retries/reopens: 20
17:43:02.339 INFO  Funcotator - Requester pays: disabled
17:43:02.339 INFO  Funcotator - Initializing engine
17:43:02.340 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
17:43:02.340 INFO  Funcotator - Done initializing engine
17:43:02.340 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:02.340 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:02.340 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder14387528741468548535/TranscriptIdFile.txt
17:43:02.340 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
17:43:02.340 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:02.341 INFO  Funcotator - Initializing data sources...
17:43:02.341 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:02.341 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:02.341 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:02.341 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:02.341 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:02.342 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.343 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:02.343 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:02.389 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:02.390 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:02.412 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:02.419 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:02.420 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:02.420 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:02.420 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:02.420 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:02.421 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
17:43:02.422 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:02.499 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:02.512 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:02.652 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:02.652 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.653 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
17:43:02.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:02.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:02.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:02.692 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.692 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:02.693 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.694 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.694 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.694 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.695 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.696 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.696 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.697 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.698 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.699 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.699 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.699 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.701 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:02.702 INFO  Funcotator - Initializing Funcotator Engine...
17:43:02.702 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:02.702 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:02.702 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.415985923217742033242.maf
17:43:02.702 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
17:43:02.703 INFO  ProgressMeter - Starting traversal
17:43:02.703 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:02.883 INFO  ProgressMeter -             unmapped              0.0                     4           1333.3
17:43:02.883 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:02.883 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:02.883 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:02.940 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:02.943 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13534617508855992180.so: /tmp/libgkl_compression13534617508855992180.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:02.943 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:02.946 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2844359164254347609.so: /tmp/libgkl_compression2844359164254347609.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:02.947 INFO  Funcotator - ------------------------------------------------------------
17:43:02.947 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:02.947 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:02.947 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:02.947 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:02.947 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:02 PM UTC
17:43:02.947 INFO  Funcotator - ------------------------------------------------------------
17:43:02.947 INFO  Funcotator - ------------------------------------------------------------
17:43:02.947 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:02.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:02.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:02.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:02.947 INFO  Funcotator - Deflater: JdkDeflater
17:43:02.947 INFO  Funcotator - Inflater: JdkInflater
17:43:02.947 INFO  Funcotator - GCS max retries/reopens: 20
17:43:02.947 INFO  Funcotator - Requester pays: disabled
17:43:02.947 INFO  Funcotator - Initializing engine
17:43:02.948 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
17:43:02.949 INFO  Funcotator - Done initializing engine
17:43:02.949 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:02.949 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:02.949 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8746007225401306773/TranscriptIdFile.txt
17:43:02.949 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
17:43:02.949 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:02.949 INFO  Funcotator - Initializing data sources...
17:43:02.949 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:02.949 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:02.949 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:02.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:02.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:02.952 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:02.952 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:02.952 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:02.952 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:03.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:03.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:03.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:03.042 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:03.043 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:03.043 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:03.043 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:03.043 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:03.044 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
17:43:03.045 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:03.121 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
17:43:03.134 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:03.272 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:03.272 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
17:43:03.273 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
17:43:03.312 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:03.312 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:03.313 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:03.313 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:03.314 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
17:43:03.314 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:03.314 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.315 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.315 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.315 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.316 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.317 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.317 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.317 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.319 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.320 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.320 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.321 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.321 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.322 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.323 INFO  Funcotator - Initializing Funcotator Engine...
17:43:03.323 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
17:43:03.323 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:03.323 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:03.323 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:03.323 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:03.324 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:03.324 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:03.324 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.36822449147361262267.maf
17:43:03.324 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
17:43:03.325 INFO  ProgressMeter - Starting traversal
17:43:03.325 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:03.359 INFO  ProgressMeter -             unmapped              0.0                     3           5294.1
17:43:03.359 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:03.359 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:03.359 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:03.413 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:03.416 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4632073167374086630.so: /tmp/libgkl_compression4632073167374086630.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:03.416 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:03.419 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4175533699282427573.so: /tmp/libgkl_compression4175533699282427573.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:03.420 INFO  Funcotator - ------------------------------------------------------------
17:43:03.420 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:03.420 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:03.420 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:03.420 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:03.420 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:03 PM UTC
17:43:03.420 INFO  Funcotator - ------------------------------------------------------------
17:43:03.420 INFO  Funcotator - ------------------------------------------------------------
17:43:03.420 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:03.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:03.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:03.420 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:03.420 INFO  Funcotator - Deflater: JdkDeflater
17:43:03.420 INFO  Funcotator - Inflater: JdkInflater
17:43:03.420 INFO  Funcotator - GCS max retries/reopens: 20
17:43:03.420 INFO  Funcotator - Requester pays: disabled
17:43:03.420 INFO  Funcotator - Initializing engine
17:43:03.421 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
17:43:03.422 INFO  Funcotator - Done initializing engine
17:43:03.422 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:03.422 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:03.422 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9955459945541634637/TranscriptIdFile.txt
17:43:03.422 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
17:43:03.422 INFO  FuncotatorEngine - Transcript parsing complete.
17:43:03.422 INFO  Funcotator - Initializing data sources...
17:43:03.422 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:03.422 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:03.422 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:03.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:03.424 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:03.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.425 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:03.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:03.469 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:03.470 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/hg19/simple_uniprot_Dec012014.tsv
17:43:03.491 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:03.498 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:03.498 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
17:43:03.499 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:03.499 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:03.499 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:03.500 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
17:43:03.501 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
17:43:03.577 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:03.589 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:03.726 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:03.726 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:03.727 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
17:43:03.766 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:03.766 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:03.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:03.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:03.768 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.768 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:03.768 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.769 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.769 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.770 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.771 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.771 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.771 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.772 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.773 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.774 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:03.774 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.774 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.776 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:03.777 INFO  Funcotator - Initializing Funcotator Engine...
17:43:03.777 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:03.777 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:03.777 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.417277590857603442571.maf
17:43:03.777 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
17:43:03.778 INFO  ProgressMeter - Starting traversal
17:43:03.778 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:03.955 INFO  ProgressMeter -             unmapped              0.0                     4           1355.9
17:43:03.955 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:03.955 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:03.955 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:03 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:04.014 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:04.017 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression795514995918921208.so: /tmp/libgkl_compression795514995918921208.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:04.017 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:04.019 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5189684735404962333.so: /tmp/libgkl_compression5189684735404962333.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:04.021 INFO  Funcotator - ------------------------------------------------------------
17:43:04.021 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:04.021 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:04.021 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:04.021 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:04.021 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:04 PM UTC
17:43:04.021 INFO  Funcotator - ------------------------------------------------------------
17:43:04.021 INFO  Funcotator - ------------------------------------------------------------
17:43:04.021 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:04.021 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:04.021 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:04.021 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:04.021 INFO  Funcotator - Deflater: JdkDeflater
17:43:04.021 INFO  Funcotator - Inflater: JdkInflater
17:43:04.021 INFO  Funcotator - GCS max retries/reopens: 20
17:43:04.021 INFO  Funcotator - Requester pays: disabled
17:43:04.021 INFO  Funcotator - Initializing engine
17:43:04.023 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.024 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
17:43:04.025 INFO  Funcotator - Done initializing engine
17:43:04.025 INFO  Funcotator - Validating sequence dictionaries...
17:43:04.025 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:04.025 INFO  Funcotator - Initializing data sources...
17:43:04.025 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:04.025 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:04.026 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
17:43:04.026 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:04.026 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
17:43:04.026 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
17:43:04.026 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
17:43:04.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:04.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:04.027 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
17:43:04.027 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
17:43:04.027 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
17:43:04.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:04.027 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
17:43:04.028 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:04.028 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:04.028 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:04.028 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:04.028 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
17:43:04.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:04.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:04.095 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:04.102 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:04.103 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:04.103 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:04.103 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:04.103 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:04.104 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
17:43:04.105 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:04.182 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:04.194 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:04.333 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:04.333 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:04.334 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
17:43:04.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:04.373 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:04.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:04.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:04.374 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:04.375 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:04.375 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.376 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:04.376 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.376 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.377 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.378 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:04.378 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.378 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.379 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.381 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.381 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:04.381 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.382 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.383 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:04.384 INFO  Funcotator - Initializing Funcotator Engine...
17:43:04.384 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:04.384 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.
17:43:04.384 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator669191348567194292.vcf
17:43:04.386 INFO  ProgressMeter - Starting traversal
17:43:04.386 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:07.732 INFO  ProgressMeter -             unmapped              0.1                   198           3550.5
17:43:07.732 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:07.732 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:07.742 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2810183680
17:43:07.744 WARN  gatk -   VCF Elapsed Time: 3.785675229s
17:43:07.744 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator669191348567194292.vcf
17:43:07.747 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
17:43:07.806 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:07.809 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7271295464559727251.so: /tmp/libgkl_compression7271295464559727251.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:07.809 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:07.812 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3396426055153019963.so: /tmp/libgkl_compression3396426055153019963.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:07.813 INFO  Funcotator - ------------------------------------------------------------
17:43:07.813 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:07.813 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:07.813 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:07.813 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:07.813 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:07 PM UTC
17:43:07.813 INFO  Funcotator - ------------------------------------------------------------
17:43:07.813 INFO  Funcotator - ------------------------------------------------------------
17:43:07.813 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:07.813 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:07.813 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:07.813 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:07.813 INFO  Funcotator - Deflater: JdkDeflater
17:43:07.813 INFO  Funcotator - Inflater: JdkInflater
17:43:07.813 INFO  Funcotator - GCS max retries/reopens: 20
17:43:07.813 INFO  Funcotator - Requester pays: disabled
17:43:07.813 INFO  Funcotator - Initializing engine
17:43:07.815 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:07.815 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
17:43:07.817 INFO  Funcotator - Done initializing engine
17:43:07.817 INFO  Funcotator - Validating sequence dictionaries...
17:43:07.817 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:07.817 INFO  Funcotator - Initializing data sources...
17:43:07.817 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:07.817 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:07.817 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:07.818 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:07.819 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
17:43:07.819 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
17:43:07.819 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
17:43:07.820 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
17:43:07.820 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:07.820 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:07.864 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:07.865 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:07.886 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:07.893 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:07.894 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:07.894 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:07.894 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:07.894 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:07.895 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
17:43:07.896 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:07.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:07.984 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:08.121 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:08.122 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:08.123 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
17:43:08.160 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:08.161 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:08.161 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:08.161 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:08.162 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:08.162 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:08.162 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.163 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:08.163 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.163 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.164 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.165 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:08.165 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.165 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.167 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.168 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.169 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:08.169 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.169 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.170 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:08.171 INFO  Funcotator - Initializing Funcotator Engine...
17:43:08.171 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:08.171 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.
17:43:08.171 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator629961007155028482.maf
17:43:08.171 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
17:43:08.172 INFO  ProgressMeter - Starting traversal
17:43:08.172 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:11.359 INFO  ProgressMeter -             unmapped              0.1                   198           3727.6
17:43:11.359 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:11.359 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:11.359 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:11 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2810183680
17:43:11.359 WARN  gatk -   MAF Elapsed Time: 3.607686188s
17:43:11.417 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:11.420 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11792323235546150661.so: /tmp/libgkl_compression11792323235546150661.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:11.421 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:11.423 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8754051390259257075.so: /tmp/libgkl_compression8754051390259257075.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:11.424 INFO  Funcotator - ------------------------------------------------------------
17:43:11.424 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:11.424 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:11.424 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:11.424 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:11.425 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:11 PM UTC
17:43:11.425 INFO  Funcotator - ------------------------------------------------------------
17:43:11.425 INFO  Funcotator - ------------------------------------------------------------
17:43:11.425 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:11.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:11.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:11.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:11.425 INFO  Funcotator - Deflater: JdkDeflater
17:43:11.425 INFO  Funcotator - Inflater: JdkInflater
17:43:11.425 INFO  Funcotator - GCS max retries/reopens: 20
17:43:11.425 INFO  Funcotator - Requester pays: disabled
17:43:11.425 INFO  Funcotator - Initializing engine
17:43:11.426 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.428 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
17:43:11.429 INFO  Funcotator - Done initializing engine
17:43:11.429 INFO  Funcotator - Validating sequence dictionaries...
17:43:11.429 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:11.429 INFO  Funcotator - Initializing data sources...
17:43:11.429 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:11.429 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:11.430 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:11.430 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:11.430 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:11.430 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:11.430 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:11.431 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:11.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:11.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:11.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:11.432 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:11.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:11.488 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:11.489 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
17:43:11.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:11.518 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:11.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:11.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:11.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:11.519 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:11.520 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
17:43:11.521 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:11.598 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:11.611 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:11.749 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:11.750 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:11.751 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
17:43:11.790 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:11.790 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:11.790 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:11.791 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:11.791 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:11.791 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:11.791 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.792 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:11.792 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.792 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.794 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.795 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
17:43:11.795 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.795 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.796 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.797 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.798 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:11.798 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.798 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.799 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:11.800 INFO  Funcotator - Initializing Funcotator Engine...
17:43:11.801 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:11.801 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.
17:43:11.801 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator15181566953672660699.vcf
17:43:11.802 INFO  ProgressMeter - Starting traversal
17:43:11.802 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:13.328 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
17:43:13.329 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
17:43:14.662 INFO  ProgressMeter -             unmapped              0.0                   168           3524.5
17:43:14.662 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
17:43:14.662 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
17:43:14.669 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:14 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2810183680
17:43:14.669 WARN  gatk -   VCF Elapsed Time: 3.307208055s
17:43:14.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator15181566953672660699.vcf
17:43:14.672 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
17:43:14.730 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:14.732 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2565105992364010052.so: /tmp/libgkl_compression2565105992364010052.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:14.733 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:14.735 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9179431641909789019.so: /tmp/libgkl_compression9179431641909789019.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:14.736 INFO  Funcotator - ------------------------------------------------------------
17:43:14.736 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:14.736 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:14.736 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:14.736 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:14.736 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:14 PM UTC
17:43:14.736 INFO  Funcotator - ------------------------------------------------------------
17:43:14.736 INFO  Funcotator - ------------------------------------------------------------
17:43:14.737 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:14.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:14.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:14.737 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:14.737 INFO  Funcotator - Deflater: JdkDeflater
17:43:14.737 INFO  Funcotator - Inflater: JdkInflater
17:43:14.737 INFO  Funcotator - GCS max retries/reopens: 20
17:43:14.737 INFO  Funcotator - Requester pays: disabled
17:43:14.737 INFO  Funcotator - Initializing engine
17:43:14.738 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:14.739 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
17:43:14.740 INFO  Funcotator - Done initializing engine
17:43:14.740 INFO  Funcotator - Validating sequence dictionaries...
17:43:14.741 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:14.741 INFO  Funcotator - Initializing data sources...
17:43:14.741 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:14.741 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:14.741 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:14.741 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:14.741 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:14.741 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:14.742 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:14.743 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
17:43:14.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:14.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:14.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:14.743 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:14.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:14.810 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:14.810 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:14.832 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:14.838 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:14.839 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:14.839 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:14.839 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:14.839 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:14.840 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
17:43:14.841 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:14.918 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:14.930 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:15.068 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:15.069 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:15.069 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
17:43:15.109 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:15.109 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:15.109 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:15.110 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:15.110 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:15.110 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:15.110 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.111 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:15.111 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.111 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.113 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:15.114 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.114 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.115 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.116 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.117 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:15.117 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.117 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.118 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:15.119 INFO  Funcotator - Initializing Funcotator Engine...
17:43:15.120 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:15.120 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.
17:43:15.120 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator11186470989519600506.maf
17:43:15.120 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
17:43:15.121 INFO  ProgressMeter - Starting traversal
17:43:15.121 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:16.646 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
17:43:16.646 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
17:43:17.927 INFO  ProgressMeter -             unmapped              0.0                   168           3592.3
17:43:17.927 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
17:43:17.927 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
17:43:17.928 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:17 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2810183680
17:43:17.928 WARN  gatk -   MAF Elapsed Time: 3.251651399s
17:43:17.983 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:17.986 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10026066058536110096.so: /tmp/libgkl_compression10026066058536110096.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:17.986 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:17.989 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17111326867569289382.so: /tmp/libgkl_compression17111326867569289382.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:17.990 INFO  Funcotator - ------------------------------------------------------------
17:43:17.990 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:17.990 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:17.990 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:17.990 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:17.990 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:17 PM UTC
17:43:17.990 INFO  Funcotator - ------------------------------------------------------------
17:43:17.990 INFO  Funcotator - ------------------------------------------------------------
17:43:17.990 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:17.990 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:17.990 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:17.990 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:17.990 INFO  Funcotator - Deflater: JdkDeflater
17:43:17.990 INFO  Funcotator - Inflater: JdkInflater
17:43:17.990 INFO  Funcotator - GCS max retries/reopens: 20
17:43:17.990 INFO  Funcotator - Requester pays: disabled
17:43:17.990 INFO  Funcotator - Initializing engine
17:43:17.992 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:17.993 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
17:43:17.994 INFO  Funcotator - Done initializing engine
17:43:17.994 INFO  Funcotator - Validating sequence dictionaries...
17:43:17.994 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:17.994 INFO  Funcotator - Initializing data sources...
17:43:17.994 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:17.994 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:17.995 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:17.996 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:17.997 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:17.997 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:17.997 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:17.997 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:18.051 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:18.051 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:18.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:18.080 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:18.080 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:18.080 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:18.081 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:18.081 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:18.082 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
17:43:18.082 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:18.158 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:18.171 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:18.309 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:18.309 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
17:43:18.310 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
17:43:18.348 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:18.348 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:18.349 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:18.349 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:18.349 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.349 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:18.350 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.350 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.351 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.351 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.352 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.353 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.353 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.353 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.354 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.355 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.356 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.356 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.356 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.357 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.358 INFO  Funcotator - Initializing Funcotator Engine...
17:43:18.359 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:18.359 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.
17:43:18.359 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator4283148798115189683.vcf
17:43:18.360 INFO  ProgressMeter - Starting traversal
17:43:18.360 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:18.376 INFO  ProgressMeter -             unmapped              0.0                     1           3750.0
17:43:18.376 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:18.376 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:18.378 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:18 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:18.378 WARN  gatk -   VCF Elapsed Time: 0.447844936s
17:43:18.379 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator4283148798115189683.vcf
17:43:18.380 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
17:43:18.435 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:18.438 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17769076940367836294.so: /tmp/libgkl_compression17769076940367836294.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:18.438 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:18.441 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7947106561791564575.so: /tmp/libgkl_compression7947106561791564575.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:18.442 INFO  Funcotator - ------------------------------------------------------------
17:43:18.442 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:18.442 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:18.442 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:18.442 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:18.442 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:18 PM UTC
17:43:18.442 INFO  Funcotator - ------------------------------------------------------------
17:43:18.442 INFO  Funcotator - ------------------------------------------------------------
17:43:18.442 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:18.442 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:18.442 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:18.442 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:18.442 INFO  Funcotator - Deflater: JdkDeflater
17:43:18.442 INFO  Funcotator - Inflater: JdkInflater
17:43:18.442 INFO  Funcotator - GCS max retries/reopens: 20
17:43:18.442 INFO  Funcotator - Requester pays: disabled
17:43:18.442 INFO  Funcotator - Initializing engine
17:43:18.444 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.445 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
17:43:18.446 INFO  Funcotator - Done initializing engine
17:43:18.446 INFO  Funcotator - Validating sequence dictionaries...
17:43:18.447 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:18.447 INFO  Funcotator - Initializing data sources...
17:43:18.447 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:18.447 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:18.447 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:18.447 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:18.447 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:18.447 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:18.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:18.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:18.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:18.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:18.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.449 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:18.449 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:18.495 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:18.496 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:18.538 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:18.545 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:18.546 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:18.546 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:18.546 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:18.546 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:18.547 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
17:43:18.548 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:18.625 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:18.637 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
17:43:18.775 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:18.775 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:18.776 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
17:43:18.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:18.814 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:18.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:18.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:18.816 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.816 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:18.816 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.817 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.817 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.817 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.818 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.819 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.819 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.820 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.822 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.822 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:18.823 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.823 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.824 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.825 INFO  Funcotator - Initializing Funcotator Engine...
17:43:18.825 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:18.825 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.
17:43:18.825 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator14273805102067723930.maf
17:43:18.825 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
17:43:18.826 INFO  ProgressMeter - Starting traversal
17:43:18.826 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:18.842 INFO  ProgressMeter -             unmapped              0.0                     1           3750.0
17:43:18.842 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:18.842 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:18.842 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:18 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:18.842 WARN  gatk -   MAF Elapsed Time: 0.461327626s
17:43:18.899 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:18.902 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4989426944043551819.so: /tmp/libgkl_compression4989426944043551819.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:18.902 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:18.904 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8920329527350553656.so: /tmp/libgkl_compression8920329527350553656.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:18.905 INFO  Funcotator - ------------------------------------------------------------
17:43:18.905 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:18.905 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:18.905 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:18.905 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:18.906 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:18 PM UTC
17:43:18.906 INFO  Funcotator - ------------------------------------------------------------
17:43:18.906 INFO  Funcotator - ------------------------------------------------------------
17:43:18.906 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:18.906 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:18.906 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:18.906 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:18.906 INFO  Funcotator - Deflater: JdkDeflater
17:43:18.906 INFO  Funcotator - Inflater: JdkInflater
17:43:18.906 INFO  Funcotator - GCS max retries/reopens: 20
17:43:18.906 INFO  Funcotator - Requester pays: disabled
17:43:18.906 INFO  Funcotator - Initializing engine
17:43:18.930 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:18.931 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
17:43:18.956 INFO  Funcotator - Done initializing engine
17:43:18.956 INFO  Funcotator - Validating sequence dictionaries...
17:43:18.964 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:18.965 INFO  Funcotator - Initializing data sources...
17:43:18.965 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:18.965 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:18.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
17:43:18.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
17:43:18.965 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/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
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
17:43:18.966 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v90_38.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
17:43:18.967 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
17:43:18.967 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
17:43:18.967 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/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
17:43:18.967 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
17:43:18.967 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:18.967 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
17:43:19.026 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/hg38/simple_uniprot_Dec012014.tsv
17:43:19.048 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/hg38/cosmic_tissue.tsv
17:43:19.055 INFO  DataSourceUtils - Resolved data source file path: file:///home/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
17:43:19.055 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.055 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:19.056 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
17:43:19.056 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:19.057 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
17:43:19.057 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
17:43:19.058 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
17:43:19.078 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
17:43:19.214 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.215 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/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
17:43:19.215 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
17:43:19.215 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:19.215 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.216 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
17:43:19.216 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.216 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.217 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.218 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
17:43:19.218 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.218 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.218 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.219 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.220 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
17:43:19.220 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.220 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.221 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.222 INFO  Funcotator - Initializing Funcotator Engine...
17:43:19.226 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:19.226 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator15430423245304376453.vcf
17:43:19.239 INFO  ProgressMeter - Starting traversal
17:43:19.239 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:19.274 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.
17:43:19.277 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
17:43:19.280 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.285 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.286 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.286 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.286 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.286 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.287 INFO  ProgressMeter -             unmapped              0.0                     5           6250.0
17:43:19.287 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
17:43:19.287 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:19.303 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:19 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:19.304 WARN  gatk -   VCF Elapsed Time: 0.460333906s
17:43:19.304 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator15430423245304376453.vcf
17:43:19.315 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
17:43:19.379 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:19.382 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15094046597360796379.so: /tmp/libgkl_compression15094046597360796379.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:19.382 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:19.384 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12300737652903737383.so: /tmp/libgkl_compression12300737652903737383.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:19.385 INFO  Funcotator - ------------------------------------------------------------
17:43:19.386 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:19.386 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:19.386 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:19.386 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:19.386 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:19 PM UTC
17:43:19.386 INFO  Funcotator - ------------------------------------------------------------
17:43:19.386 INFO  Funcotator - ------------------------------------------------------------
17:43:19.386 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:19.386 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:19.386 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:19.386 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:19.386 INFO  Funcotator - Deflater: JdkDeflater
17:43:19.386 INFO  Funcotator - Inflater: JdkInflater
17:43:19.386 INFO  Funcotator - GCS max retries/reopens: 20
17:43:19.386 INFO  Funcotator - Requester pays: disabled
17:43:19.386 INFO  Funcotator - Initializing engine
17:43:19.410 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.411 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
17:43:19.435 INFO  Funcotator - Done initializing engine
17:43:19.435 INFO  Funcotator - Validating sequence dictionaries...
17:43:19.444 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:19.444 INFO  Funcotator - Initializing data sources...
17:43:19.444 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:19.444 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:19.444 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/hg38/hgnc_download_Nov302017.tsv
17:43:19.444 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/hg38/simple_uniprot_Dec012014.tsv
17:43:19.445 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:19.445 INFO  DataSourceUtils - Resolved data source file path: file:///home/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
17:43:19.445 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.445 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/hg38/cosmic_fusion.tsv
17:43:19.445 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
17:43:19.445 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
17:43:19.446 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
17:43:19.446 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
17:43:19.446 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.446 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/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
17:43:19.446 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
17:43:19.446 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:19.446 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/hg38/hgnc_download_Nov302017.tsv
17:43:19.512 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.534 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
17:43:19.541 INFO  DataSourceUtils - Resolved data source file path: file:///home/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
17:43:19.542 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:19.542 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:19.542 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
17:43:19.542 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:19.543 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
17:43:19.544 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
17:43:19.545 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
17:43:19.565 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
17:43:19.700 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
17:43:19.700 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:19.701 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
17:43:19.701 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:19.701 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.702 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
17:43:19.702 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.702 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.702 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.703 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
17:43:19.703 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.704 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.704 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.705 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.706 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
17:43:19.706 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.706 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.706 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.707 INFO  Funcotator - Initializing Funcotator Engine...
17:43:19.711 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:19.711 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator16190226051386636796.maf
17:43:19.713 INFO  ProgressMeter - Starting traversal
17:43:19.713 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:19.743 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.
17:43:19.743 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
17:43:19.746 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.751 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.751 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
17:43:19.751 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.751 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.751 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
17:43:19.752 INFO  ProgressMeter -             unmapped              0.0                     5           7692.3
17:43:19.752 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
17:43:19.752 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:19.752 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:19 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2810183680
17:43:19.752 WARN  gatk -   MAF Elapsed Time: 0.429431282s
17:43:19.810 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:19.813 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression867378679008990455.so: /tmp/libgkl_compression867378679008990455.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:19.813 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:19.816 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7660617648681386240.so: /tmp/libgkl_compression7660617648681386240.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:19.817 INFO  Funcotator - ------------------------------------------------------------
17:43:19.817 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:19.817 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:19.817 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:19.817 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:19.817 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:19 PM UTC
17:43:19.817 INFO  Funcotator - ------------------------------------------------------------
17:43:19.817 INFO  Funcotator - ------------------------------------------------------------
17:43:19.817 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:19.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:19.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:19.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:19.817 INFO  Funcotator - Deflater: JdkDeflater
17:43:19.817 INFO  Funcotator - Inflater: JdkInflater
17:43:19.817 INFO  Funcotator - GCS max retries/reopens: 20
17:43:19.817 INFO  Funcotator - Requester pays: disabled
17:43:19.817 INFO  Funcotator - Initializing engine
17:43:19.819 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:19.820 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
17:43:19.822 INFO  Funcotator - Done initializing engine
17:43:19.822 INFO  Funcotator - Validating sequence dictionaries...
17:43:19.822 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:19.822 INFO  Funcotator - Initializing data sources...
17:43:19.822 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:19.822 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:19.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:19.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:19.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:19.823 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:19.824 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:19.825 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:19.825 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:19.825 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:19.825 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:19.825 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:19.825 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:19.871 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:19.872 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:19.894 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:19.901 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:19.901 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:19.901 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
17:43:19.902 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:19.902 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:19.903 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
17:43:19.903 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:20.014 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:20.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:20.167 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:20.168 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:20.168 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
17:43:20.207 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:20.207 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:20.208 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:20.208 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:20.209 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:20.209 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:20.209 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.210 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:20.210 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.210 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.211 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.212 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:20.212 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.212 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.214 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.215 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.215 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:20.216 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.216 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.217 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:20.218 INFO  Funcotator - Initializing Funcotator Engine...
17:43:20.218 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:20.218 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.
17:43:20.218 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator13899953813650624147.vcf
17:43:20.222 INFO  ProgressMeter - Starting traversal
17:43:20.222 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:27.832 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
17:43:27.833 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
17:43:27.834 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          11878.6
17:43:27.834 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
17:43:27.834 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
17:43:27.860 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:27 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=2810183680
17:43:27.860 WARN  gatk -   VCF Elapsed Time: 8.105742083s
17:43:27.861 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator13899953813650624147.vcf
17:43:27.870 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
17:43:27.945 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:27.948 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13814815864058201161.so: /tmp/libgkl_compression13814815864058201161.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:27.948 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:27.951 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression18221240064848663859.so: /tmp/libgkl_compression18221240064848663859.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:27.952 INFO  Funcotator - ------------------------------------------------------------
17:43:27.952 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:27.952 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:27.952 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:27.952 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:27.952 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:27 PM UTC
17:43:27.952 INFO  Funcotator - ------------------------------------------------------------
17:43:27.952 INFO  Funcotator - ------------------------------------------------------------
17:43:27.952 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:27.952 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:27.952 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:27.952 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:27.952 INFO  Funcotator - Deflater: JdkDeflater
17:43:27.952 INFO  Funcotator - Inflater: JdkInflater
17:43:27.952 INFO  Funcotator - GCS max retries/reopens: 20
17:43:27.952 INFO  Funcotator - Requester pays: disabled
17:43:27.952 INFO  Funcotator - Initializing engine
17:43:27.954 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:27.955 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
17:43:27.956 INFO  Funcotator - Done initializing engine
17:43:27.956 INFO  Funcotator - Validating sequence dictionaries...
17:43:27.956 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:27.957 INFO  Funcotator - Initializing data sources...
17:43:27.957 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:27.957 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:27.957 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
17:43:27.957 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
17:43:27.957 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:27.957 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:27.958 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
17:43:27.958 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
17:43:27.958 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
17:43:27.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:27.958 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
17:43:27.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:27.958 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:27.959 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
17:43:27.959 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
17:43:27.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:27.959 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:27.959 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:27.959 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
17:43:28.004 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:28.005 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:28.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:28.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:28.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:28.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:28.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:28.035 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:28.036 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
17:43:28.037 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:28.114 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:28.177 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:28.346 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:28.346 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
17:43:28.347 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
17:43:28.386 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
17:43:28.386 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
WARNING	2025-10-27 17:43:28	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:28.387 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
17:43:28.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:28.387 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:28.387 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:28.388 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.389 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
17:43:28.389 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.389 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.390 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.391 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
17:43:28.391 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.391 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.392 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.393 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.394 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
17:43:28.394 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.394 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.395 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:28.396 INFO  Funcotator - Initializing Funcotator Engine...
17:43:28.397 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:28.397 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.
17:43:28.397 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator2483811121517413692.maf
17:43:28.397 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
17:43:28.398 INFO  ProgressMeter - Starting traversal
17:43:28.398 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:35.549 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
17:43:35.549 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
17:43:35.550 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          12642.6
17:43:35.550 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
17:43:35.550 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
17:43:35.550 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:35 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=2810183680
17:43:35.550 WARN  gatk -   MAF Elapsed Time: 7.658885336s
17:43:35.618 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:35.622 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1979585011338045575.so: /tmp/libgkl_compression1979585011338045575.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:35.622 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:35.625 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2823357136750375281.so: /tmp/libgkl_compression2823357136750375281.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:35.626 INFO  Funcotator - ------------------------------------------------------------
17:43:35.626 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:35.626 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:35.626 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:35.626 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:35.626 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:35 PM UTC
17:43:35.626 INFO  Funcotator - ------------------------------------------------------------
17:43:35.626 INFO  Funcotator - ------------------------------------------------------------
17:43:35.626 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:35.626 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:35.626 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:35.626 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:35.626 INFO  Funcotator - Deflater: JdkDeflater
17:43:35.626 INFO  Funcotator - Inflater: JdkInflater
17:43:35.626 INFO  Funcotator - GCS max retries/reopens: 20
17:43:35.626 INFO  Funcotator - Requester pays: disabled
17:43:35.626 INFO  Funcotator - Initializing engine
17:43:35.628 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:35.629 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
17:43:35.630 INFO  Funcotator - Done initializing engine
17:43:35.631 INFO  Funcotator - Validating sequence dictionaries...
17:43:35.631 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:35.631 INFO  Funcotator - Initializing data sources...
17:43:35.631 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:35.631 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:35.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:35.631 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:35.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:35.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:35.632 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
17:43:35.632 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
17:43:35.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:35.632 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
17:43:35.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:35.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:35.633 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
17:43:35.633 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:35.633 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:35.633 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:35.633 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:35.633 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:35.633 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:35.680 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:35.680 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:35.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:35.710 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:35.710 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:35.710 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:35.711 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:35.711 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:35.712 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:35.712 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:35.829 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:35.842 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:36.008 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:36.009 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:36.009 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
17:43:36.049 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
17:43:36.049 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
WARNING	2025-10-27 17:43:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:36.049 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
17:43:36.050 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:36.050 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:36.050 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:36.050 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.051 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:36.051 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.051 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.053 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.054 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:36.054 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.054 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.055 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.056 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.057 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:36.057 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.057 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.058 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:36.059 INFO  Funcotator - Initializing Funcotator Engine...
17:43:36.060 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:36.060 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.
17:43:36.060 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator2344883041434335444.vcf
17:43:36.061 INFO  ProgressMeter - Starting traversal
17:43:36.061 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:39.282 INFO  ProgressMeter -             unmapped              0.1                   198           3688.3
17:43:39.282 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:39.282 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:39.293 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:39 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2982150144
17:43:39.348 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:39.351 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2964239416679514895.so: /tmp/libgkl_compression2964239416679514895.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:39.351 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:39.354 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5257328524802046116.so: /tmp/libgkl_compression5257328524802046116.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:39.355 INFO  Funcotator - ------------------------------------------------------------
17:43:39.355 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:39.355 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:39.355 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:39.355 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:39.355 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:39 PM UTC
17:43:39.355 INFO  Funcotator - ------------------------------------------------------------
17:43:39.355 INFO  Funcotator - ------------------------------------------------------------
17:43:39.355 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:39.355 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:39.355 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:39.355 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:39.355 INFO  Funcotator - Deflater: JdkDeflater
17:43:39.355 INFO  Funcotator - Inflater: JdkInflater
17:43:39.355 INFO  Funcotator - GCS max retries/reopens: 20
17:43:39.355 INFO  Funcotator - Requester pays: disabled
17:43:39.355 INFO  Funcotator - Initializing engine
17:43:39.357 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.358 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
17:43:39.359 INFO  Funcotator - Done initializing engine
17:43:39.359 INFO  Funcotator - Validating sequence dictionaries...
17:43:39.359 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:39.359 INFO  Funcotator - Initializing data sources...
17:43:39.359 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:39.359 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:39.361 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:39.361 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:39.361 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:39.362 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:39.363 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:39.363 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:39.432 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:39.433 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:39.455 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
17:43:39.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:39.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:39.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:39.463 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:39.463 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:39.464 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
17:43:39.464 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:39.540 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:39.552 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:39.690 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:39.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:39.691 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
17:43:39.730 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:39.730 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:39.731 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:39.731 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:39.731 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:39.731 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:39.732 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.732 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:39.733 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.733 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.734 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.735 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:39.735 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.735 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.736 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.737 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.738 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:39.738 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.738 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.740 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:39.741 INFO  Funcotator - Initializing Funcotator Engine...
17:43:39.741 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:39.741 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.
17:43:39.741 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator5781118178144267835.maf
17:43:39.741 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
17:43:39.742 INFO  ProgressMeter - Starting traversal
17:43:39.742 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:42.871 INFO  ProgressMeter -             unmapped              0.1                   198           3796.7
17:43:42.872 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:42.872 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:42.872 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2982150144
17:43:42.927 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:42.930 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13772358692270788845.so: /tmp/libgkl_compression13772358692270788845.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:42.930 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:42.933 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2382340225397368196.so: /tmp/libgkl_compression2382340225397368196.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:42.934 INFO  Funcotator - ------------------------------------------------------------
17:43:42.934 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:42.934 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:42.934 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:42.934 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:42.934 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:42 PM UTC
17:43:42.934 INFO  Funcotator - ------------------------------------------------------------
17:43:42.934 INFO  Funcotator - ------------------------------------------------------------
17:43:42.934 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:42.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:42.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:42.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:42.935 INFO  Funcotator - Deflater: JdkDeflater
17:43:42.935 INFO  Funcotator - Inflater: JdkInflater
17:43:42.935 INFO  Funcotator - GCS max retries/reopens: 20
17:43:42.935 INFO  Funcotator - Requester pays: disabled
17:43:42.935 INFO  Funcotator - Initializing engine
17:43:42.936 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:42.937 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
17:43:42.938 INFO  Funcotator - Done initializing engine
17:43:42.938 INFO  Funcotator - Validating sequence dictionaries...
17:43:42.938 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:42.939 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:42.994 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:42.997 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11534063630878056103.so: /tmp/libgkl_compression11534063630878056103.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:42.997 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.000 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1889497210151803550.so: /tmp/libgkl_compression1889497210151803550.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.001 INFO  Funcotator - ------------------------------------------------------------
17:43:43.001 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:43.001 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:43.001 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:43.001 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:43.001 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:42 PM UTC
17:43:43.001 INFO  Funcotator - ------------------------------------------------------------
17:43:43.001 INFO  Funcotator - ------------------------------------------------------------
17:43:43.001 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:43.001 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:43.001 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:43.001 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:43.001 INFO  Funcotator - Deflater: JdkDeflater
17:43:43.001 INFO  Funcotator - Inflater: JdkInflater
17:43:43.001 INFO  Funcotator - GCS max retries/reopens: 20
17:43:43.001 INFO  Funcotator - Requester pays: disabled
17:43:43.001 INFO  Funcotator - Initializing engine
17:43:43.003 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
17:43:43.020 INFO  Funcotator - Done initializing engine
17:43:43.020 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:43.020 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:43.020 INFO  Funcotator - Initializing data sources...
17:43:43.020 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:43.020 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:43.020 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
17:43:43.021 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
17:43:43.021 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
17:43:43.021 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:43.021 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
17:43:43.021 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:43.022 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
17:43:43.022 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
17:43:43.022 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
17:43:43.023 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:43.023 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
17:43:43.031 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
17:43:43.040 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
17:43:43.049 INFO  Funcotator - Initializing Funcotator Engine...
17:43:43.054 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:43.054 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14049005888431653672.vcf
17:43:43.066 INFO  ProgressMeter - Starting traversal
17:43:43.067 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:43.098 INFO  ProgressMeter -             unmapped              0.0                   100         193548.4
17:43:43.098 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
17:43:43.098 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:43.105 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:43.106 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14049005888431653672.vcf
17:43:43.174 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.177 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2157922270241933175.so: /tmp/libgkl_compression2157922270241933175.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.177 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.180 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13355733631934758690.so: /tmp/libgkl_compression13355733631934758690.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.181 INFO  Funcotator - ------------------------------------------------------------
17:43:43.181 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:43.181 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:43.181 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:43.181 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:43.181 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:43 PM UTC
17:43:43.181 INFO  Funcotator - ------------------------------------------------------------
17:43:43.181 INFO  Funcotator - ------------------------------------------------------------
17:43:43.181 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:43.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:43.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:43.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:43.181 INFO  Funcotator - Deflater: JdkDeflater
17:43:43.181 INFO  Funcotator - Inflater: JdkInflater
17:43:43.181 INFO  Funcotator - GCS max retries/reopens: 20
17:43:43.181 INFO  Funcotator - Requester pays: disabled
17:43:43.181 INFO  Funcotator - Initializing engine
17:43:43.183 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
17:43:43.185 INFO  Funcotator - Done initializing engine
17:43:43.185 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:43.185 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:43.185 INFO  Funcotator - Initializing data sources...
17:43:43.185 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:43.185 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:43.185 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
17:43:43.185 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
17:43:43.185 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
17:43:43.185 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:43.185 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
17:43:43.185 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:43.186 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
17:43:43.186 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:43.187 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:43.187 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:43.187 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
17:43:43.188 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:43.190 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:43.190 INFO  Funcotator - Initializing Funcotator Engine...
17:43:43.190 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:43.191 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
17:43:43.191 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1350995988383625119.vcf
17:43:43.194 INFO  ProgressMeter - Starting traversal
17:43:43.194 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:43.204 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
17:43:43.204 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
17:43:43.204 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:43:43.207 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:43.208 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1350995988383625119.vcf
17:43:43.265 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.268 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13566130870794019347.so: /tmp/libgkl_compression13566130870794019347.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.268 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.271 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17410448405565130852.so: /tmp/libgkl_compression17410448405565130852.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.272 INFO  Funcotator - ------------------------------------------------------------
17:43:43.272 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:43.272 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:43.272 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:43.272 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:43.272 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:43 PM UTC
17:43:43.272 INFO  Funcotator - ------------------------------------------------------------
17:43:43.272 INFO  Funcotator - ------------------------------------------------------------
17:43:43.272 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:43.272 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:43.272 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:43.272 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:43.272 INFO  Funcotator - Deflater: JdkDeflater
17:43:43.272 INFO  Funcotator - Inflater: JdkInflater
17:43:43.272 INFO  Funcotator - GCS max retries/reopens: 20
17:43:43.272 INFO  Funcotator - Requester pays: disabled
17:43:43.272 INFO  Funcotator - Initializing engine
17:43:43.274 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
17:43:43.286 INFO  Funcotator - Done initializing engine
17:43:43.286 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:43.286 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:43.286 INFO  Funcotator - Initializing data sources...
17:43:43.286 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:43.286 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:43.286 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
17:43:43.286 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
17:43:43.286 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
17:43:43.286 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:43.286 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
17:43:43.286 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:43.287 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
17:43:43.287 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
17:43:43.288 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
17:43:43.288 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:43.289 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
17:43:43.296 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
17:43:43.305 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
17:43:43.313 INFO  Funcotator - Initializing Funcotator Engine...
17:43:43.317 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:43.317 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5789592644902971401.vcf
17:43:43.328 INFO  ProgressMeter - Starting traversal
17:43:43.328 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:43.340 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)
17:43:43.340 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)
17:43:43.340 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.340 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:43.340 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
17:43:43.340 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
17:43:43.343 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.344 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:43.344 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
17:43:43.344 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
17:43:43.344 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)
17:43:43.345 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)
17:43:43.345 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.345 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:43.345 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
17:43:43.345 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
17:43:43.346 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)
17:43:43.346 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)
17:43:43.346 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
17:43:43.346 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
17:43:43.346 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
17:43:43.346 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
17:43:43.347 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.347 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:43.347 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
17:43:43.347 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
17:43:43.348 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.348 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:43.348 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
17:43:43.348 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
17:43:43.349 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)
17:43:43.349 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)
17:43:43.349 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
17:43:43.349 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:43.349 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
17:43:43.349 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
17:43:43.350 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)
17:43:43.350 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)
17:43:43.350 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.350 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:43.350 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
17:43:43.350 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
17:43:43.351 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
17:43:43.351 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:43.351 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
17:43:43.352 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
17:43:43.352 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)
17:43:43.352 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)
17:43:43.352 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:43.352 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:43.353 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
17:43:43.353 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
17:43:43.353 INFO  ProgressMeter -             unmapped              0.0                    10          24000.0
17:43:43.353 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
17:43:43.353 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:43.359 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:43.360 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out5789592644902971401.vcf
17:43:43.426 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.429 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17971462815793140501.so: /tmp/libgkl_compression17971462815793140501.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.429 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.432 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression123331313363008466.so: /tmp/libgkl_compression123331313363008466.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.433 INFO  Funcotator - ------------------------------------------------------------
17:43:43.433 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:43.433 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:43.433 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:43.433 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:43.433 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:43 PM UTC
17:43:43.433 INFO  Funcotator - ------------------------------------------------------------
17:43:43.433 INFO  Funcotator - ------------------------------------------------------------
17:43:43.433 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:43.433 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:43.433 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:43.433 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:43.433 INFO  Funcotator - Deflater: JdkDeflater
17:43:43.433 INFO  Funcotator - Inflater: JdkInflater
17:43:43.433 INFO  Funcotator - GCS max retries/reopens: 20
17:43:43.433 INFO  Funcotator - Requester pays: disabled
17:43:43.433 INFO  Funcotator - Initializing engine
17:43:43.435 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.436 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
17:43:43.438 INFO  Funcotator - Done initializing engine
17:43:43.438 INFO  Funcotator - Validating sequence dictionaries...
17:43:43.438 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:43.438 INFO  Funcotator - Initializing data sources...
17:43:43.438 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:43.438 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:43.438 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:43.439 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:43.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:43.440 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:43.441 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:43.487 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:43.487 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:43.509 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:43.516 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:43.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:43.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:43.517 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:43.518 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:43.519 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
17:43:43.519 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:43.597 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:43.610 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:43.748 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:43.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:43.749 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
17:43:43.788 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
17:43:43.789 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:43.789 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:43.789 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
17:43:43.790 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
17:43:43.790 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:43.790 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.791 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
17:43:43.791 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.791 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.792 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.793 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:43.793 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.793 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.795 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.796 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.797 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:43.797 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.797 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.798 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.799 INFO  Funcotator - Initializing Funcotator Engine...
17:43:43.799 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:43.799 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.
17:43:43.799 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator15302626271209945495.vcf
17:43:43.803 INFO  ProgressMeter - Starting traversal
17:43:43.803 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:43.884 INFO  ProgressMeter -             unmapped              0.0                     1            740.7
17:43:43.884 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:43.884 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:43.885 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:43.885 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator15302626271209945495.vcf
17:43:43.941 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.944 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression893131578628673136.so: /tmp/libgkl_compression893131578628673136.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.944 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:43.947 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6321314539090163313.so: /tmp/libgkl_compression6321314539090163313.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:43.948 INFO  Funcotator - ------------------------------------------------------------
17:43:43.948 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:43.948 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:43.948 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:43.948 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:43.948 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:43 PM UTC
17:43:43.948 INFO  Funcotator - ------------------------------------------------------------
17:43:43.948 INFO  Funcotator - ------------------------------------------------------------
17:43:43.948 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:43.948 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:43.948 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:43.948 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:43.948 INFO  Funcotator - Deflater: JdkDeflater
17:43:43.948 INFO  Funcotator - Inflater: JdkInflater
17:43:43.948 INFO  Funcotator - GCS max retries/reopens: 20
17:43:43.948 INFO  Funcotator - Requester pays: disabled
17:43:43.948 INFO  Funcotator - Initializing engine
17:43:43.950 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:43.951 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
17:43:43.952 INFO  Funcotator - Done initializing engine
17:43:43.952 INFO  Funcotator - Validating sequence dictionaries...
17:43:43.953 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:43.953 INFO  Funcotator - Initializing data sources...
17:43:43.953 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:43.953 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:43.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:43.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:43.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:43.953 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:43.954 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:43.955 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:43.955 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:43.955 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:43.955 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:43.955 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:43.955 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:44.000 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:44.001 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
17:43:44.023 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:44.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:44.031 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:44.031 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:44.031 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:44.031 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:44.032 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
17:43:44.033 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:44.108 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:44.120 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:44.259 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:44.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:44.261 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
17:43:44.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:44.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:44.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:44.300 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:44.300 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
17:43:44.300 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:44.300 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.301 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.301 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.301 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.302 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.303 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.303 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.303 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.305 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.306 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.306 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.307 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.307 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.308 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.309 INFO  Funcotator - Initializing Funcotator Engine...
17:43:44.309 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:44.309 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.
17:43:44.309 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator6893253624090300202.vcf
17:43:44.313 INFO  ProgressMeter - Starting traversal
17:43:44.313 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:44.319 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
17:43:44.433 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.433 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.433 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.433 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.434 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.434 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.434 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
17:43:44.439 INFO  ProgressMeter -             unmapped              0.0                     2            952.4
17:43:44.439 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
17:43:44.439 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:44.440 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:44.441 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator6893253624090300202.vcf
17:43:44.499 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:44.501 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7248954177683866781.so: /tmp/libgkl_compression7248954177683866781.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:44.502 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:44.504 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12065956217927377303.so: /tmp/libgkl_compression12065956217927377303.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:44.505 INFO  Funcotator - ------------------------------------------------------------
17:43:44.505 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:44.505 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:44.505 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:44.505 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:44.505 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:44 PM UTC
17:43:44.505 INFO  Funcotator - ------------------------------------------------------------
17:43:44.505 INFO  Funcotator - ------------------------------------------------------------
17:43:44.505 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:44.505 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:44.506 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:44.506 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:44.506 INFO  Funcotator - Deflater: JdkDeflater
17:43:44.506 INFO  Funcotator - Inflater: JdkInflater
17:43:44.506 INFO  Funcotator - GCS max retries/reopens: 20
17:43:44.506 INFO  Funcotator - Requester pays: disabled
17:43:44.506 INFO  Funcotator - Initializing engine
17:43:44.507 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.508 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
17:43:44.509 INFO  Funcotator - Done initializing engine
17:43:44.509 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:44.509 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:44.509 INFO  Funcotator - Initializing data sources...
17:43:44.509 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:44.509 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:44.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:44.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:44.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:44.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:44.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:44.511 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
17:43:44.511 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
17:43:44.511 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:44.512 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
17:43:44.512 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:44.512 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:44.557 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:44.558 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:44.579 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:44.586 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:44.587 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:44.587 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:44.587 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:44.587 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:44.588 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
17:43:44.589 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:44.664 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:44.677 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:44.814 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:44.815 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:44.816 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
17:43:44.854 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:44.854 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:44.854 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:44.855 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:44.855 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.855 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:44.855 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.856 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.856 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.856 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.858 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.859 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.859 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.859 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.860 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.861 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.862 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:44.862 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.862 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.863 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:44.864 INFO  Funcotator - Initializing Funcotator Engine...
17:43:44.864 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:44.864 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.
17:43:44.865 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
17:43:44.865 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
17:43:44.865 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
17:43:44.865 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8683652619318245172.vcf
17:43:44.868 INFO  ProgressMeter - Starting traversal
17:43:44.868 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:44.925 INFO  ProgressMeter -             unmapped              0.0                     1           1052.6
17:43:44.925 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:44.925 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:44.926 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:44 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:44.927 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8683652619318245172.vcf
17:43:44.928 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
[October 27, 2025 at 5:43:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
[October 27, 2025 at 5:43:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:45.161 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.164 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4030749338992981457.so: /tmp/libgkl_compression4030749338992981457.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.164 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.167 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13081607969490396898.so: /tmp/libgkl_compression13081607969490396898.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.168 INFO  Funcotator - ------------------------------------------------------------
17:43:45.168 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:45.168 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:45.168 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:45.168 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:45.168 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:45 PM UTC
17:43:45.168 INFO  Funcotator - ------------------------------------------------------------
17:43:45.168 INFO  Funcotator - ------------------------------------------------------------
17:43:45.168 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:45.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:45.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:45.168 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:45.168 INFO  Funcotator - Deflater: JdkDeflater
17:43:45.168 INFO  Funcotator - Inflater: JdkInflater
17:43:45.168 INFO  Funcotator - GCS max retries/reopens: 20
17:43:45.168 INFO  Funcotator - Requester pays: disabled
17:43:45.168 INFO  Funcotator - Initializing engine
17:43:45.169 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
17:43:45.184 INFO  Funcotator - Done initializing engine
17:43:45.184 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:45.184 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:45.184 INFO  Funcotator - Initializing data sources...
17:43:45.184 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:45.185 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:45.185 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
17:43:45.185 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
17:43:45.185 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
17:43:45.185 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:45.185 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
17:43:45.185 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:45.186 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
17:43:45.186 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
17:43:45.187 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
17:43:45.187 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:45.187 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
17:43:45.195 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
17:43:45.204 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
17:43:45.212 INFO  Funcotator - Initializing Funcotator Engine...
17:43:45.219 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:45.219 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7692452058761621102.vcf
17:43:45.231 INFO  ProgressMeter - Starting traversal
17:43:45.231 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:45.262 INFO  ProgressMeter -             unmapped              0.0                   100         193548.4
17:43:45.262 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
17:43:45.262 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:45.269 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:45.270 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7692452058761621102.vcf
17:43:45.341 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.344 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11020578389972670249.so: /tmp/libgkl_compression11020578389972670249.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.344 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.347 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression18208386601810908947.so: /tmp/libgkl_compression18208386601810908947.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.348 INFO  Funcotator - ------------------------------------------------------------
17:43:45.348 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:45.348 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:45.348 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:45.348 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:45.348 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:45 PM UTC
17:43:45.348 INFO  Funcotator - ------------------------------------------------------------
17:43:45.348 INFO  Funcotator - ------------------------------------------------------------
17:43:45.348 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:45.348 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:45.348 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:45.348 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:45.348 INFO  Funcotator - Deflater: JdkDeflater
17:43:45.348 INFO  Funcotator - Inflater: JdkInflater
17:43:45.348 INFO  Funcotator - GCS max retries/reopens: 20
17:43:45.348 INFO  Funcotator - Requester pays: disabled
17:43:45.348 INFO  Funcotator - Initializing engine
17:43:45.350 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.351 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
17:43:45.352 INFO  Funcotator - Done initializing engine
17:43:45.352 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:45.352 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:45.352 INFO  Funcotator - Initializing data sources...
17:43:45.352 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/
17:43:45.352 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:45.353 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
17:43:45.353 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
17:43:45.353 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
17:43:45.353 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:45.353 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
17:43:45.353 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:45.354 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
17:43:45.354 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:45.354 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
17:43:45.354 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
17:43:45.354 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.355 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
17:43:45.355 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.355 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.357 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.358 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
17:43:45.358 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.358 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.359 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.360 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.361 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
17:43:45.361 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.361 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.362 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.364 INFO  Funcotator - Initializing Funcotator Engine...
17:43:45.364 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:45.364 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.
17:43:45.364 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:45.364 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing15316590587207506558.vcf
17:43:45.366 INFO  ProgressMeter - Starting traversal
17:43:45.366 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:45.403 INFO  ProgressMeter -             unmapped              0.0                     1           1621.6
17:43:45.403 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:45.403 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
17:43:45.406 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:45.407 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing15316590587207506558.vcf
17:43:45.465 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.467 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10304164840955688705.so: /tmp/libgkl_compression10304164840955688705.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.468 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.470 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8595811467286865782.so: /tmp/libgkl_compression8595811467286865782.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.471 INFO  Funcotator - ------------------------------------------------------------
17:43:45.471 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:45.471 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:45.471 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:45.472 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:45.472 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:45 PM UTC
17:43:45.472 INFO  Funcotator - ------------------------------------------------------------
17:43:45.472 INFO  Funcotator - ------------------------------------------------------------
17:43:45.472 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:45.472 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:45.472 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:45.472 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:45.472 INFO  Funcotator - Deflater: JdkDeflater
17:43:45.472 INFO  Funcotator - Inflater: JdkInflater
17:43:45.472 INFO  Funcotator - GCS max retries/reopens: 20
17:43:45.472 INFO  Funcotator - Requester pays: disabled
17:43:45.472 INFO  Funcotator - Initializing engine
17:43:45.473 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
17:43:45.474 INFO  Funcotator - Done initializing engine
17:43:45.474 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:45.474 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:45.474 INFO  Funcotator - Initializing data sources...
17:43:45.474 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:45.474 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:45.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:45.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:45.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:45.474 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:45.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:45.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:45.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:45.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:45.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:45.476 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:45.476 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:45.535 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:45.536 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
17:43:45.558 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
17:43:45.565 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:45.565 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
17:43:45.565 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
17:43:45.566 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:45.566 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:45.567 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
17:43:45.567 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:45.643 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:45.656 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:45.794 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:45.794 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:45.795 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
17:43:45.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:45.834 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:45.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:45.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:45.835 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:45.835 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:45.836 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.836 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:45.837 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.837 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.838 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.839 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
17:43:45.839 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.839 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.840 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.841 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.842 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:45.842 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.842 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.843 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:45.844 INFO  Funcotator - Initializing Funcotator Engine...
17:43:45.845 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
17:43:45.845 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:45.845 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:45.845 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:45.845 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:45.846 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:45.846 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:45.846 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:45.846 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:45.846 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5075465601743435928.vcf
17:43:45.846 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
17:43:45.847 INFO  ProgressMeter - Starting traversal
17:43:45.847 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:45.880 INFO  ProgressMeter -             unmapped              0.0                     3           5454.5
17:43:45.880 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:45.880 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:45.883 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:45 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:45.940 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.942 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10879717514965128720.so: /tmp/libgkl_compression10879717514965128720.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.943 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:45.945 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11088289889650867837.so: /tmp/libgkl_compression11088289889650867837.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:45.946 INFO  Funcotator - ------------------------------------------------------------
17:43:45.947 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:45.947 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:45.947 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:45.947 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:45.947 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:45 PM UTC
17:43:45.947 INFO  Funcotator - ------------------------------------------------------------
17:43:45.947 INFO  Funcotator - ------------------------------------------------------------
17:43:45.947 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:45.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:45.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:45.947 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:45.947 INFO  Funcotator - Deflater: JdkDeflater
17:43:45.947 INFO  Funcotator - Inflater: JdkInflater
17:43:45.947 INFO  Funcotator - GCS max retries/reopens: 20
17:43:45.947 INFO  Funcotator - Requester pays: disabled
17:43:45.947 INFO  Funcotator - Initializing engine
17:43:45.948 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
17:43:45.948 INFO  Funcotator - Done initializing engine
17:43:45.948 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:45.948 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:45.948 INFO  Funcotator - Initializing data sources...
17:43:45.948 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:45.948 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:45.949 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:45.949 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:45.949 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:45.949 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:45.950 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:45.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:45.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:45.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:45.951 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:45.951 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:45.997 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:45.997 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:46.019 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:46.026 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
17:43:46.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:46.027 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:46.027 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
17:43:46.027 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:46.028 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
17:43:46.029 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:46.104 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:46.117 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:46.257 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:46.257 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:46.258 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
17:43:46.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:46.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:46.298 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:46.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:46.299 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.299 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:46.299 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.300 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.300 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.300 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.301 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.302 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.303 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.303 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.304 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.305 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.306 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.306 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.306 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.307 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.308 INFO  Funcotator - Initializing Funcotator Engine...
17:43:46.308 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:46.308 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:46.308 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13066328571492036632.vcf
17:43:46.309 INFO  ProgressMeter - Starting traversal
17:43:46.309 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:46.545 INFO  ProgressMeter -             unmapped              0.0                     4           1016.9
17:43:46.546 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:46.546 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:46.546 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:46 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:46.603 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:46.606 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1878096614232035448.so: /tmp/libgkl_compression1878096614232035448.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:46.606 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:46.609 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9930779881905318118.so: /tmp/libgkl_compression9930779881905318118.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:46.610 INFO  Funcotator - ------------------------------------------------------------
17:43:46.610 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:46.610 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:46.610 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:46.610 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:46.610 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:46 PM UTC
17:43:46.610 INFO  Funcotator - ------------------------------------------------------------
17:43:46.610 INFO  Funcotator - ------------------------------------------------------------
17:43:46.610 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:46.610 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:46.610 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:46.610 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:46.610 INFO  Funcotator - Deflater: JdkDeflater
17:43:46.610 INFO  Funcotator - Inflater: JdkInflater
17:43:46.610 INFO  Funcotator - GCS max retries/reopens: 20
17:43:46.610 INFO  Funcotator - Requester pays: disabled
17:43:46.610 INFO  Funcotator - Initializing engine
17:43:46.611 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
17:43:46.612 INFO  Funcotator - Done initializing engine
17:43:46.612 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:46.612 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:46.612 INFO  Funcotator - Initializing data sources...
17:43:46.612 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:46.612 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:46.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:46.612 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:46.612 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
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:46.613 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:46.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:46.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:46.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:46.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.614 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:46.614 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:46.660 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
17:43:46.661 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:46.682 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:46.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:46.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:46.689 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:46.690 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:46.690 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:46.691 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
17:43:46.691 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:46.767 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:46.780 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:46.918 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:46.919 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:46.920 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
17:43:46.959 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
17:43:46.959 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
WARNING	2025-10-27 17:43:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:46.959 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
17:43:46.960 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
17:43:46.960 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
17:43:46.960 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:46.960 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.961 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.961 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.961 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.962 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.963 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.964 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.964 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.965 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.966 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.967 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:46.967 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.967 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.968 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:46.969 INFO  Funcotator - Initializing Funcotator Engine...
17:43:46.969 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
17:43:46.969 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:46.969 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:46.969 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:46.969 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:46.970 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:46.970 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:46.970 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16507568255031087463.vcf
17:43:46.970 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
17:43:46.971 INFO  ProgressMeter - Starting traversal
17:43:46.971 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:47.004 INFO  ProgressMeter -             unmapped              0.0                     3           5454.5
17:43:47.004 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:47.005 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:47.007 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:47.063 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:47.066 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1900434720766691835.so: /tmp/libgkl_compression1900434720766691835.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:47.067 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:47.069 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13405010623216055825.so: /tmp/libgkl_compression13405010623216055825.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:47.071 INFO  Funcotator - ------------------------------------------------------------
17:43:47.071 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:47.071 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:47.071 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:47.071 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:47.071 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:47 PM UTC
17:43:47.071 INFO  Funcotator - ------------------------------------------------------------
17:43:47.071 INFO  Funcotator - ------------------------------------------------------------
17:43:47.071 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:47.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:47.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:47.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:47.071 INFO  Funcotator - Deflater: JdkDeflater
17:43:47.071 INFO  Funcotator - Inflater: JdkInflater
17:43:47.071 INFO  Funcotator - GCS max retries/reopens: 20
17:43:47.071 INFO  Funcotator - Requester pays: disabled
17:43:47.071 INFO  Funcotator - Initializing engine
17:43:47.072 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
17:43:47.073 INFO  Funcotator - Done initializing engine
17:43:47.073 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:47.073 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:47.073 INFO  Funcotator - Initializing data sources...
17:43:47.073 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:47.073 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:47.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:47.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:47.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:47.075 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:47.075 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:47.075 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
17:43:47.075 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
17:43:47.075 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:47.075 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
17:43:47.121 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:47.122 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:47.163 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:47.170 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:47.170 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:47.170 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:47.171 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:47.171 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:47.172 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
17:43:47.172 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:47.249 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:47.262 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:47.401 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:47.402 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:47.402 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
17:43:47.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:47.442 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:47.443 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:47.443 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:47.443 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:47.443 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:47.444 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.445 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:47.445 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.445 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.446 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.447 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:47.447 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.447 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.448 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.449 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.450 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:47.450 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.450 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.452 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:47.453 INFO  Funcotator - Initializing Funcotator Engine...
17:43:47.453 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:47.453 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:47.453 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2848758038146035991.vcf
17:43:47.454 INFO  ProgressMeter - Starting traversal
17:43:47.454 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:47.629 INFO  ProgressMeter -             unmapped              0.0                     4           1371.4
17:43:47.629 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:47.629 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:47.630 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:47 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:47.686 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:47.689 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6106184392672147926.so: /tmp/libgkl_compression6106184392672147926.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:47.689 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:47.692 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression18121993153595389162.so: /tmp/libgkl_compression18121993153595389162.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:47.693 INFO  Funcotator - ------------------------------------------------------------
17:43:47.693 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:47.693 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:47.693 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:47.693 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:47.693 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:47 PM UTC
17:43:47.693 INFO  Funcotator - ------------------------------------------------------------
17:43:47.693 INFO  Funcotator - ------------------------------------------------------------
17:43:47.693 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:47.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:47.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:47.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:47.694 INFO  Funcotator - Deflater: JdkDeflater
17:43:47.694 INFO  Funcotator - Inflater: JdkInflater
17:43:47.694 INFO  Funcotator - GCS max retries/reopens: 20
17:43:47.694 INFO  Funcotator - Requester pays: disabled
17:43:47.694 INFO  Funcotator - Initializing engine
17:43:47.695 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
17:43:47.695 INFO  Funcotator - Done initializing engine
17:43:47.695 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:47.695 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:47.695 INFO  Funcotator - Initializing data sources...
17:43:47.695 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:47.695 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:47.696 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:47.697 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:47.698 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:47.698 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:47.698 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:47.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:47.743 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:47.765 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:47.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:47.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:47.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:47.773 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:47.773 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:47.774 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
17:43:47.774 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:47.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:47.862 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:48.032 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:48.032 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.033 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
17:43:48.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:48.073 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:48.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:48.074 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.074 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:48.074 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.075 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.075 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.075 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.076 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.077 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
17:43:48.078 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.078 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.079 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.080 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.081 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
17:43:48.081 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.081 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.082 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.083 INFO  Funcotator - Initializing Funcotator Engine...
17:43:48.083 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
17:43:48.084 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:48.084 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:48.084 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:48.084 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:48.084 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:48.084 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16890657268576235169.maf
17:43:48.085 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
17:43:48.085 INFO  ProgressMeter - Starting traversal
17:43:48.085 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:48.117 INFO  ProgressMeter -             unmapped              0.0                     3           5625.0
17:43:48.117 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:48.117 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:48.117 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:48 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:48.173 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:48.176 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17444758208967014620.so: /tmp/libgkl_compression17444758208967014620.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:48.176 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:48.179 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4478488793214224404.so: /tmp/libgkl_compression4478488793214224404.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:48.180 INFO  Funcotator - ------------------------------------------------------------
17:43:48.180 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:48.180 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:48.180 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:48.180 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:48.180 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:48 PM UTC
17:43:48.180 INFO  Funcotator - ------------------------------------------------------------
17:43:48.180 INFO  Funcotator - ------------------------------------------------------------
17:43:48.180 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:48.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:48.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:48.180 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:48.180 INFO  Funcotator - Deflater: JdkDeflater
17:43:48.180 INFO  Funcotator - Inflater: JdkInflater
17:43:48.180 INFO  Funcotator - GCS max retries/reopens: 20
17:43:48.180 INFO  Funcotator - Requester pays: disabled
17:43:48.180 INFO  Funcotator - Initializing engine
17:43:48.181 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
17:43:48.182 INFO  Funcotator - Done initializing engine
17:43:48.182 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:48.182 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:48.182 INFO  Funcotator - Initializing data sources...
17:43:48.182 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:48.182 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:48.182 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:48.182 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:48.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:48.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:48.183 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/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:48.183 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/hg19/dnaRepairGenes.20171221T103938.csv
17:43:48.183 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/hg19/cosmic_fusion.tsv
17:43:48.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:48.183 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
17:43:48.183 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.184 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:48.184 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:48.230 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:48.230 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:48.252 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:48.258 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:48.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:48.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:48.259 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:48.259 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:48.260 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
17:43:48.261 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:48.336 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:48.348 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:48.486 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:48.486 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.487 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
17:43:48.526 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.526 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:48.527 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:48.527 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:48.528 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.528 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:48.528 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.529 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.529 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.529 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.530 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.531 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.531 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.532 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.533 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.534 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:48.534 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.534 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.536 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:48.537 INFO  Funcotator - Initializing Funcotator Engine...
17:43:48.537 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:48.537 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:48.537 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5290451702042776774.maf
17:43:48.537 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
17:43:48.537 INFO  ProgressMeter - Starting traversal
17:43:48.537 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:48.758 INFO  ProgressMeter -             unmapped              0.0                     4           1086.0
17:43:48.758 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:48.758 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:48.758 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:48 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:48.812 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:48.814 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11082467030909235115.so: /tmp/libgkl_compression11082467030909235115.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:48.815 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:48.817 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6686297632670861023.so: /tmp/libgkl_compression6686297632670861023.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:48.818 INFO  Funcotator - ------------------------------------------------------------
17:43:48.818 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:48.818 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:48.818 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:48.818 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:48.818 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:48 PM UTC
17:43:48.818 INFO  Funcotator - ------------------------------------------------------------
17:43:48.818 INFO  Funcotator - ------------------------------------------------------------
17:43:48.818 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:48.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:48.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:48.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:48.818 INFO  Funcotator - Deflater: JdkDeflater
17:43:48.818 INFO  Funcotator - Inflater: JdkInflater
17:43:48.818 INFO  Funcotator - GCS max retries/reopens: 20
17:43:48.818 INFO  Funcotator - Requester pays: disabled
17:43:48.818 INFO  Funcotator - Initializing engine
17:43:48.819 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
17:43:48.820 INFO  Funcotator - Done initializing engine
17:43:48.820 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:48.820 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:48.820 INFO  Funcotator - Initializing data sources...
17:43:48.820 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:48.820 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:48.820 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:48.821 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:48.822 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
17:43:48.822 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:48.822 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:48.867 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:48.867 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:48.888 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:48.895 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:48.895 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:48.896 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:48.896 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:48.896 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:48.897 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
17:43:48.897 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:48.972 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:48.985 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:49.123 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:49.123 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:49.124 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
17:43:49.163 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:49.164 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:49.164 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:49.164 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:49.165 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.165 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:49.165 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.166 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.166 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.166 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.214 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.215 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.215 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.215 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.216 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.217 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.218 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.218 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.218 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.220 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.221 INFO  Funcotator - Initializing Funcotator Engine...
17:43:49.221 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
17:43:49.221 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:43:49.221 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:43:49.221 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:43:49.221 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:43:49.222 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:43:49.222 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:49.222 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16136219373630990889.maf
17:43:49.222 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
17:43:49.222 INFO  ProgressMeter - Starting traversal
17:43:49.222 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:49.253 INFO  ProgressMeter -             unmapped              0.0                     3           5806.5
17:43:49.253 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
17:43:49.253 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:49.253 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:49.310 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:49.313 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1626647285480203797.so: /tmp/libgkl_compression1626647285480203797.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:49.313 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:49.315 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10401287856698950784.so: /tmp/libgkl_compression10401287856698950784.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:49.316 INFO  Funcotator - ------------------------------------------------------------
17:43:49.316 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:49.316 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:49.317 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:49.317 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:49.317 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:49 PM UTC
17:43:49.317 INFO  Funcotator - ------------------------------------------------------------
17:43:49.317 INFO  Funcotator - ------------------------------------------------------------
17:43:49.317 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:49.317 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:49.317 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:49.317 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:49.317 INFO  Funcotator - Deflater: JdkDeflater
17:43:49.317 INFO  Funcotator - Inflater: JdkInflater
17:43:49.317 INFO  Funcotator - GCS max retries/reopens: 20
17:43:49.317 INFO  Funcotator - Requester pays: disabled
17:43:49.317 INFO  Funcotator - Initializing engine
17:43:49.318 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
17:43:49.318 INFO  Funcotator - Done initializing engine
17:43:49.318 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:49.318 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:49.318 INFO  Funcotator - Initializing data sources...
17:43:49.318 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:49.318 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:49.319 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:49.320 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:49.321 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.321 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:49.321 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:49.368 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:49.368 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:49.390 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:49.397 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:49.397 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:49.397 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:49.398 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:49.398 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:49.399 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
17:43:49.399 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:49.475 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:49.488 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:49.626 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:49.627 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:49.627 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
17:43:49.667 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:49.667 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:49.667 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:49.668 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:49.668 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.668 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:49.668 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.669 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.669 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.669 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.670 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.671 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.672 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.672 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.673 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.674 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.675 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:49.675 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.675 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.676 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:49.677 INFO  Funcotator - Initializing Funcotator Engine...
17:43:49.677 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:49.677 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:49.677 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8320525805134071760.maf
17:43:49.677 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
17:43:49.678 INFO  ProgressMeter - Starting traversal
17:43:49.678 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:49.897 INFO  ProgressMeter -             unmapped              0.0                     4           1095.9
17:43:49.897 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
17:43:49.897 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
17:43:49.898 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:49 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2982150144
17:43:49.953 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:49.956 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17013111143068478982.so: /tmp/libgkl_compression17013111143068478982.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:49.956 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:49.958 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2192956076533290487.so: /tmp/libgkl_compression2192956076533290487.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:49.959 INFO  Funcotator - ------------------------------------------------------------
17:43:49.959 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:49.959 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:49.959 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:49.959 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:49.959 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:49 PM UTC
17:43:49.959 INFO  Funcotator - ------------------------------------------------------------
17:43:49.959 INFO  Funcotator - ------------------------------------------------------------
17:43:49.960 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:49.960 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:49.960 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:49.960 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:49.960 INFO  Funcotator - Deflater: JdkDeflater
17:43:49.960 INFO  Funcotator - Inflater: JdkInflater
17:43:49.960 INFO  Funcotator - GCS max retries/reopens: 20
17:43:49.960 INFO  Funcotator - Requester pays: disabled
17:43:49.960 INFO  Funcotator - Initializing engine
17:43:49.961 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
17:43:49.984 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
17:43:49.984 INFO  Funcotator - Done initializing engine
17:43:49.984 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:49.984 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:49.984 INFO  Funcotator - Initializing data sources...
17:43:49.984 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/
17:43:49.984 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:49.985 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
17:43:49.985 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
17:43:49.985 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
17:43:49.985 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:49.985 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
17:43:49.985 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:49.986 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
17:43:49.986 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
17:43:49.986 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
17:43:49.986 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:49.987 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
17:43:49.995 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
17:43:50.004 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
17:43:50.012 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.016 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:50.016 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4921302803197281757.vcf
17:43:50.029 INFO  ProgressMeter - Starting traversal
17:43:50.029 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.043 INFO  ProgressMeter -             unmapped              0.0                    32         137142.9
17:43:50.043 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
17:43:50.043 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:50.050 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.106 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.109 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17633768253623015355.so: /tmp/libgkl_compression17633768253623015355.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.109 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.112 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression16990077566526995249.so: /tmp/libgkl_compression16990077566526995249.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.113 INFO  Funcotator - ------------------------------------------------------------
17:43:50.113 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.113 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.113 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.113 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.113 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.113 INFO  Funcotator - ------------------------------------------------------------
17:43:50.113 INFO  Funcotator - ------------------------------------------------------------
17:43:50.113 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.113 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.113 INFO  Funcotator - Inflater: JdkInflater
17:43:50.113 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.113 INFO  Funcotator - Requester pays: disabled
17:43:50.113 INFO  Funcotator - Initializing engine
17:43:50.114 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
17:43:50.135 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
17:43:50.135 INFO  Funcotator - Done initializing engine
17:43:50.135 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.135 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.135 INFO  Funcotator - Initializing data sources...
17:43:50.135 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/
17:43:50.135 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.136 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
17:43:50.136 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
17:43:50.136 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
17:43:50.136 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.136 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
17:43:50.136 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.137 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
17:43:50.137 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
17:43:50.137 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
17:43:50.137 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.138 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
17:43:50.146 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg38_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
17:43:50.154 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
17:43:50.162 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.166 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:50.166 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4554131648967769764.vcf
17:43:50.179 INFO  ProgressMeter - Starting traversal
17:43:50.179 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.192 INFO  ProgressMeter -             unmapped              0.0                    32         147692.3
17:43:50.192 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
17:43:50.192 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:50.199 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.199 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4921302803197281757.vcf
17:43:50.210 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4554131648967769764.vcf
17:43:50.277 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.280 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2686640559280868636.so: /tmp/libgkl_compression2686640559280868636.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.280 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.283 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5292129726679450979.so: /tmp/libgkl_compression5292129726679450979.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.284 INFO  Funcotator - ------------------------------------------------------------
17:43:50.284 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.284 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.284 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.284 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.284 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.284 INFO  Funcotator - ------------------------------------------------------------
17:43:50.284 INFO  Funcotator - ------------------------------------------------------------
17:43:50.284 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.284 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.284 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.284 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.284 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.284 INFO  Funcotator - Inflater: JdkInflater
17:43:50.284 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.284 INFO  Funcotator - Requester pays: disabled
17:43:50.284 INFO  Funcotator - Initializing engine
17:43:50.285 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
17:43:50.286 INFO  Funcotator - Done initializing engine
17:43:50.286 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.286 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.286 INFO  Funcotator - Initializing data sources...
17:43:50.286 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.286 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.287 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
17:43:50.287 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
17:43:50.287 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
17:43:50.287 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.287 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
17:43:50.287 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.288 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
17:43:50.288 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
17:43:50.288 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
17:43:50.288 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.289 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
17:43:50.290 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
17:43:50.291 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
17:43:50.292 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.292 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.292 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.
17:43:50.292 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12631490694302246701.maf
17:43:50.293 INFO  ProgressMeter - Starting traversal
17:43:50.293 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.295 WARN  MafOutputRenderer - 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
17:43:50.295 WARN  MafOutputRenderer - 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
17:43:50.296 WARN  MafOutputRenderer - 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
17:43:50.297 WARN  MafOutputRenderer - 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=
17:43:50.298 WARN  MafOutputRenderer - 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=
17:43:50.299 WARN  MafOutputRenderer - 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=
17:43:50.299 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
17:43:50.299 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
17:43:50.299 WARN  Funcotator - ================================================================================
17:43:50.299 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:43:50.299 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:43:50.299 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:43:50.299 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:43:50.299 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:43:50.299 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:43:50.299 WARN  Funcotator - --------------------------------------------------------------------------------
17:43:50.299 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:43:50.299 WARN  Funcotator -  run was misconfigured.     
17:43:50.299 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:43:50.299 WARN  Funcotator - ================================================================================
17:43:50.299 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.299 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.357 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.360 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10444516639144517418.so: /tmp/libgkl_compression10444516639144517418.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.360 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.363 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4566062525759623209.so: /tmp/libgkl_compression4566062525759623209.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.364 INFO  Funcotator - ------------------------------------------------------------
17:43:50.364 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.364 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.364 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.364 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.364 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.364 INFO  Funcotator - ------------------------------------------------------------
17:43:50.364 INFO  Funcotator - ------------------------------------------------------------
17:43:50.364 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.364 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.364 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.364 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.364 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.364 INFO  Funcotator - Inflater: JdkInflater
17:43:50.364 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.364 INFO  Funcotator - Requester pays: disabled
17:43:50.364 INFO  Funcotator - Initializing engine
17:43:50.366 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
17:43:50.367 INFO  Funcotator - Done initializing engine
17:43:50.367 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.367 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.367 INFO  Funcotator - Initializing data sources...
17:43:50.367 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.367 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.367 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
17:43:50.367 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
17:43:50.367 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
17:43:50.367 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.367 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
17:43:50.367 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.368 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
17:43:50.368 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
17:43:50.369 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
17:43:50.369 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.369 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
17:43:50.370 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
17:43:50.371 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
17:43:50.372 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.372 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.372 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.
17:43:50.373 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7854984563511306630.maf
17:43:50.373 INFO  ProgressMeter - Starting traversal
17:43:50.373 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.375 WARN  MafOutputRenderer - 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
17:43:50.375 WARN  MafOutputRenderer - 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
17:43:50.376 WARN  MafOutputRenderer - 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
17:43:50.377 WARN  MafOutputRenderer - 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=
17:43:50.377 WARN  MafOutputRenderer - 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=
17:43:50.379 WARN  MafOutputRenderer - 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=
17:43:50.379 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
17:43:50.379 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
17:43:50.379 WARN  Funcotator - ================================================================================
17:43:50.379 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:43:50.379 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:43:50.379 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:43:50.379 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:43:50.379 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:43:50.379 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:43:50.379 WARN  Funcotator - --------------------------------------------------------------------------------
17:43:50.379 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:43:50.379 WARN  Funcotator -  run was misconfigured.     
17:43:50.379 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:43:50.379 WARN  Funcotator - ================================================================================
17:43:50.379 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.379 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.437 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.440 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6781797024908791215.so: /tmp/libgkl_compression6781797024908791215.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.440 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.443 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12195793281751485718.so: /tmp/libgkl_compression12195793281751485718.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.444 INFO  Funcotator - ------------------------------------------------------------
17:43:50.444 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.444 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.444 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.444 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.444 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.444 INFO  Funcotator - ------------------------------------------------------------
17:43:50.444 INFO  Funcotator - ------------------------------------------------------------
17:43:50.444 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.444 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.444 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.444 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.444 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.444 INFO  Funcotator - Inflater: JdkInflater
17:43:50.444 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.444 INFO  Funcotator - Requester pays: disabled
17:43:50.444 INFO  Funcotator - Initializing engine
17:43:50.445 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
17:43:50.446 INFO  Funcotator - Done initializing engine
17:43:50.446 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.446 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.446 INFO  Funcotator - Initializing data sources...
17:43:50.446 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.446 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.447 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
17:43:50.447 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
17:43:50.447 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
17:43:50.447 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.447 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
17:43:50.447 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.448 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
17:43:50.448 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
17:43:50.448 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.448 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.449 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.450 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
17:43:50.451 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
17:43:50.452 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.452 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.452 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.
17:43:50.452 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6065201525937149638.maf
17:43:50.452 INFO  ProgressMeter - Starting traversal
17:43:50.453 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.454 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 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
17:43:50.455 WARN  MafOutputRenderer - 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
17:43:50.455 WARN  MafOutputRenderer - 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
17:43:50.456 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 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=
17:43:50.457 WARN  MafOutputRenderer - 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=
17:43:50.458 WARN  MafOutputRenderer - 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=
17:43:50.458 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
17:43:50.458 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
17:43:50.458 WARN  Funcotator - ================================================================================
17:43:50.458 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:43:50.458 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:43:50.458 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:43:50.458 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:43:50.458 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:43:50.458 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:43:50.458 WARN  Funcotator - --------------------------------------------------------------------------------
17:43:50.458 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:43:50.458 WARN  Funcotator -  run was misconfigured.     
17:43:50.458 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:43:50.458 WARN  Funcotator - ================================================================================
17:43:50.458 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.458 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.516 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.519 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7242605009373262372.so: /tmp/libgkl_compression7242605009373262372.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.519 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.522 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5570204234699969594.so: /tmp/libgkl_compression5570204234699969594.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.522 INFO  Funcotator - ------------------------------------------------------------
17:43:50.523 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.523 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.523 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.523 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.523 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.523 INFO  Funcotator - ------------------------------------------------------------
17:43:50.523 INFO  Funcotator - ------------------------------------------------------------
17:43:50.523 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.523 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.523 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.523 INFO  Funcotator - Inflater: JdkInflater
17:43:50.523 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.523 INFO  Funcotator - Requester pays: disabled
17:43:50.523 INFO  Funcotator - Initializing engine
17:43:50.524 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
17:43:50.525 INFO  Funcotator - Done initializing engine
17:43:50.525 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.525 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.525 INFO  Funcotator - Initializing data sources...
17:43:50.525 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.525 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.525 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
17:43:50.525 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
17:43:50.526 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
17:43:50.526 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.526 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
17:43:50.526 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.526 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
17:43:50.527 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
17:43:50.527 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
17:43:50.527 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.528 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/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.529 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
17:43:50.530 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
17:43:50.531 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.531 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.531 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.
17:43:50.531 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7019371027171788252.maf
17:43:50.531 INFO  ProgressMeter - Starting traversal
17:43:50.531 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.533 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 @ 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
17:43:50.533 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 @ 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
17:43:50.534 WARN  MafOutputRenderer - 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
17:43:50.535 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 @ 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=
17:43:50.535 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 @ 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=
17:43:50.536 WARN  MafOutputRenderer - 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=
17:43:50.537 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
17:43:50.537 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
17:43:50.537 WARN  Funcotator - ================================================================================
17:43:50.537 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:43:50.537 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:43:50.537 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:43:50.537 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:43:50.537 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:43:50.537 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:43:50.537 WARN  Funcotator - --------------------------------------------------------------------------------
17:43:50.537 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:43:50.537 WARN  Funcotator -  run was misconfigured.     
17:43:50.537 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:43:50.537 WARN  Funcotator - ================================================================================
17:43:50.537 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.537 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.594 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.597 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9509732637200102750.so: /tmp/libgkl_compression9509732637200102750.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.597 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.600 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3946906989480370704.so: /tmp/libgkl_compression3946906989480370704.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.601 INFO  Funcotator - ------------------------------------------------------------
17:43:50.601 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.601 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.601 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.601 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.601 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.601 INFO  Funcotator - ------------------------------------------------------------
17:43:50.601 INFO  Funcotator - ------------------------------------------------------------
17:43:50.601 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.601 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.601 INFO  Funcotator - Inflater: JdkInflater
17:43:50.601 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.601 INFO  Funcotator - Requester pays: disabled
17:43:50.601 INFO  Funcotator - Initializing engine
17:43:50.602 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
17:43:50.603 INFO  Funcotator - Done initializing engine
17:43:50.603 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.603 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.603 INFO  Funcotator - Initializing data sources...
17:43:50.603 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.603 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.604 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:50.604 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:50.604 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.604 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.604 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:50.604 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.605 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:50.605 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:50.605 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.605 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.606 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.607 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.608 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:50.609 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.609 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.609 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.
17:43:50.609 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5466728701219238292.vcf
17:43:50.613 INFO  ProgressMeter - Starting traversal
17:43:50.613 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.624 INFO  ProgressMeter -             unmapped              0.0                    21         114545.5
17:43:50.624 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
17:43:50.624 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:43:50.627 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.627 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out5466728701219238292.vcf
17:43:50.713 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.716 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15171320341150140047.so: /tmp/libgkl_compression15171320341150140047.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.716 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.719 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5444581513557505739.so: /tmp/libgkl_compression5444581513557505739.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.720 INFO  Funcotator - ------------------------------------------------------------
17:43:50.720 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.720 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.720 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.720 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.720 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.720 INFO  Funcotator - ------------------------------------------------------------
17:43:50.720 INFO  Funcotator - ------------------------------------------------------------
17:43:50.720 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.720 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.720 INFO  Funcotator - Inflater: JdkInflater
17:43:50.720 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.720 INFO  Funcotator - Requester pays: disabled
17:43:50.720 INFO  Funcotator - Initializing engine
17:43:50.721 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
17:43:50.722 INFO  Funcotator - Done initializing engine
17:43:50.722 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.722 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.722 INFO  Funcotator - Initializing data sources...
17:43:50.722 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.722 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.723 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
17:43:50.723 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
17:43:50.723 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
17:43:50.723 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.723 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
17:43:50.723 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.724 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
17:43:50.724 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
17:43:50.724 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
17:43:50.724 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.725 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
17:43:50.726 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
17:43:50.727 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
17:43:50.728 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.728 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:50.728 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.
17:43:50.728 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5967818477390797884.maf
17:43:50.729 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.729 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.785 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.788 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5148613268949585270.so: /tmp/libgkl_compression5148613268949585270.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.788 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.791 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4946430622211744852.so: /tmp/libgkl_compression4946430622211744852.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.792 INFO  Funcotator - ------------------------------------------------------------
17:43:50.792 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.792 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.792 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.792 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.792 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.792 INFO  Funcotator - ------------------------------------------------------------
17:43:50.792 INFO  Funcotator - ------------------------------------------------------------
17:43:50.792 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.792 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.792 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.792 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.792 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.792 INFO  Funcotator - Inflater: JdkInflater
17:43:50.792 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.792 INFO  Funcotator - Requester pays: disabled
17:43:50.792 INFO  Funcotator - Initializing engine
17:43:50.793 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
17:43:50.805 INFO  Funcotator - Done initializing engine
17:43:50.805 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:50.805 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:50.805 INFO  Funcotator - Initializing data sources...
17:43:50.805 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:50.805 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:50.805 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
17:43:50.805 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
17:43:50.805 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
17:43:50.805 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:50.805 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
17:43:50.805 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:50.806 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
17:43:50.807 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
17:43:50.807 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
17:43:50.807 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:50.808 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
17:43:50.816 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
17:43:50.824 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
17:43:50.832 INFO  Funcotator - Initializing Funcotator Engine...
17:43:50.839 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:50.839 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12885570176823666613.maf
17:43:50.839 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
17:43:50.839 INFO  ProgressMeter - Starting traversal
17:43:50.840 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:50.842 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)
17:43:50.842 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)
17:43:50.842 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.842 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:50.842 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
17:43:50.842 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
17:43:50.844 WARN  MafOutputRenderer - 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+
17:43:50.848 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.848 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:50.848 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
17:43:50.848 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
17:43:50.848 WARN  MafOutputRenderer - 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+
17:43:50.848 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)
17:43:50.849 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)
17:43:50.849 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.849 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:50.849 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
17:43:50.849 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
17:43:50.849 WARN  MafOutputRenderer - 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+
17:43:50.849 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)
17:43:50.850 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)
17:43:50.850 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
17:43:50.850 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
17:43:50.850 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
17:43:50.850 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
17:43:50.850 WARN  MafOutputRenderer - 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+
17:43:50.851 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.851 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:50.851 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
17:43:50.851 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
17:43:50.851 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 @ 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+
17:43:50.852 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.852 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:50.852 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
17:43:50.852 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
17:43:50.852 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 @ 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=
17:43:50.852 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)
17:43:50.853 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)
17:43:50.853 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
17:43:50.853 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:50.853 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
17:43:50.853 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
17:43:50.853 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 @ 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=
17:43:50.853 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)
17:43:50.854 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)
17:43:50.854 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.854 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:50.854 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
17:43:50.854 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
17:43:50.854 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 @ 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+
17:43:50.854 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
17:43:50.855 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
17:43:50.855 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
17:43:50.855 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
17:43:50.855 WARN  MafOutputRenderer - 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+
17:43:50.855 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)
17:43:50.855 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)
17:43:50.855 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
17:43:50.855 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
17:43:50.856 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
17:43:50.856 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
17:43:50.856 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
17:43:50.856 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
17:43:50.856 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
17:43:50.856 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
17:43:50.856 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:50.986 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.989 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3707894204676448094.so: /tmp/libgkl_compression3707894204676448094.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.989 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:50.992 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5039459797599991796.so: /tmp/libgkl_compression5039459797599991796.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:50.993 INFO  Funcotator - ------------------------------------------------------------
17:43:50.993 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:50.993 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:50.993 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:50.993 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:50.993 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:50 PM UTC
17:43:50.993 INFO  Funcotator - ------------------------------------------------------------
17:43:50.993 INFO  Funcotator - ------------------------------------------------------------
17:43:50.993 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:50.993 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:50.993 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:50.993 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:50.993 INFO  Funcotator - Deflater: JdkDeflater
17:43:50.993 INFO  Funcotator - Inflater: JdkInflater
17:43:50.993 INFO  Funcotator - GCS max retries/reopens: 20
17:43:50.993 INFO  Funcotator - Requester pays: disabled
17:43:50.993 INFO  Funcotator - Initializing engine
17:43:50.994 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
17:43:50.996 INFO  Funcotator - Done initializing engine
17:43:50.996 INFO  Funcotator - Validating sequence dictionaries...
17:43:50.996 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:50 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2982150144
17:43:51.052 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:51.055 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression96447722392073479.so: /tmp/libgkl_compression96447722392073479.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:51.055 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:51.058 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14696787737235419625.so: /tmp/libgkl_compression14696787737235419625.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:51.059 INFO  Funcotator - ------------------------------------------------------------
17:43:51.059 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:51.059 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:51.059 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:51.059 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:51.059 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:51 PM UTC
17:43:51.059 INFO  Funcotator - ------------------------------------------------------------
17:43:51.059 INFO  Funcotator - ------------------------------------------------------------
17:43:51.059 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:51.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:51.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:51.059 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:51.059 INFO  Funcotator - Deflater: JdkDeflater
17:43:51.059 INFO  Funcotator - Inflater: JdkInflater
17:43:51.059 INFO  Funcotator - GCS max retries/reopens: 20
17:43:51.059 INFO  Funcotator - Requester pays: disabled
17:43:51.059 INFO  Funcotator - Initializing engine
17:43:51.061 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.062 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
17:43:51.063 INFO  Funcotator - Done initializing engine
17:43:51.063 INFO  Funcotator - Validating sequence dictionaries...
17:43:51.063 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:51.063 INFO  Funcotator - Initializing data sources...
17:43:51.063 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:51.063 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:51.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:51.063 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:51.064 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:51.065 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:51.065 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:51.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:51.112 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:51.134 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:51.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:51.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:51.141 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:51.142 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:51.142 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:51.143 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
17:43:51.143 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:51.219 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:51.231 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:51.409 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:51.410 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
17:43:51.410 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
17:43:51.450 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:51.450 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:51.451 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:51.451 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:51.452 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:51.452 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:51.452 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.453 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:51.453 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.453 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.454 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.455 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:51.455 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.455 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.456 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.458 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.458 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:51.458 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.458 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.460 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:51.461 INFO  Funcotator - Initializing Funcotator Engine...
17:43:51.461 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:51.461 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.
17:43:51.461 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator13512705710121187442.vcf
17:43:51.462 INFO  ProgressMeter - Starting traversal
17:43:51.463 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:54.625 INFO  ProgressMeter -             unmapped              0.1                   198           3757.1
17:43:54.625 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:54.626 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:54.636 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:54 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2982150144
17:43:54.691 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:54.694 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2664160882967806328.so: /tmp/libgkl_compression2664160882967806328.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:54.694 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:54.697 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5327658153690841510.so: /tmp/libgkl_compression5327658153690841510.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:54.698 INFO  Funcotator - ------------------------------------------------------------
17:43:54.698 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:54.698 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:54.698 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:54.698 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:54.698 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:54 PM UTC
17:43:54.698 INFO  Funcotator - ------------------------------------------------------------
17:43:54.698 INFO  Funcotator - ------------------------------------------------------------
17:43:54.698 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:54.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:54.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:54.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:54.698 INFO  Funcotator - Deflater: JdkDeflater
17:43:54.698 INFO  Funcotator - Inflater: JdkInflater
17:43:54.698 INFO  Funcotator - GCS max retries/reopens: 20
17:43:54.698 INFO  Funcotator - Requester pays: disabled
17:43:54.698 INFO  Funcotator - Initializing engine
17:43:54.700 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:54.701 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
17:43:54.702 INFO  Funcotator - Done initializing engine
17:43:54.702 INFO  Funcotator - Validating sequence dictionaries...
17:43:54.702 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:54.702 INFO  Funcotator - Initializing data sources...
17:43:54.702 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:54.702 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:54.702 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:54.703 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:54.704 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:54.704 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:54.750 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:54.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:54.772 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:54.779 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:54.780 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:54.780 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:54.780 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:54.780 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:54.781 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
17:43:54.782 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:54.857 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:54.870 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:55.043 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:55.043 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:55.044 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
17:43:55.083 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:55.083 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:43:55	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:55.083 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:55.084 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:55.084 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:55.084 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:55.084 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.085 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:55.085 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.086 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.087 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.088 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:55.088 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.088 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.089 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.090 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.091 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:55.091 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.091 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.092 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:55.093 INFO  Funcotator - Initializing Funcotator Engine...
17:43:55.094 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
17:43:55.094 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.
17:43:55.094 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator4687799077809957590.maf
17:43:55.094 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
17:43:55.094 INFO  ProgressMeter - Starting traversal
17:43:55.095 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.210 INFO  ProgressMeter -             unmapped              0.1                   198           3813.8
17:43:58.210 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.1 minutes.
17:43:58.210 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
17:43:58.211 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3011510272
17:43:58.267 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.270 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8801272648155193431.so: /tmp/libgkl_compression8801272648155193431.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.270 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.272 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6362266917773710408.so: /tmp/libgkl_compression6362266917773710408.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.273 INFO  Funcotator - ------------------------------------------------------------
17:43:58.273 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:58.273 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:58.273 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:58.273 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:58.273 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:58.273 INFO  Funcotator - ------------------------------------------------------------
17:43:58.273 INFO  Funcotator - ------------------------------------------------------------
17:43:58.274 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:58.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:58.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:58.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:58.274 INFO  Funcotator - Deflater: JdkDeflater
17:43:58.274 INFO  Funcotator - Inflater: JdkInflater
17:43:58.274 INFO  Funcotator - GCS max retries/reopens: 20
17:43:58.274 INFO  Funcotator - Requester pays: disabled
17:43:58.274 INFO  Funcotator - Initializing engine
17:43:58.300 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.302 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
17:43:58.322 INFO  Funcotator - Done initializing engine
17:43:58.322 INFO  Funcotator - Validating sequence dictionaries...
17:43:58.329 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:58.329 INFO  Funcotator - Initializing data sources...
17:43:58.329 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:58.329 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:58.329 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.329 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
17:43:58.329 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.329 INFO  DataSourceUtils - Resolved data source file path: file:///home/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
17:43:58.330 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:58.330 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.330 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
17:43:58.330 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
17:43:58.330 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
17:43:58.330 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
17:43:58.330 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:58.330 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/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
17:43:58.331 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
17:43:58.331 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:58.331 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.395 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:58.417 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.423 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
17:43:58.424 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:58.424 INFO  DataSourceUtils - Resolved data source file path: 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
17:43:58.424 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
17:43:58.424 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:58.425 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
17:43:58.425 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
17:43:58.426 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
17:43:58.446 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
17:43:58.580 INFO  DataSourceUtils - Resolved data source file path: file:///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
17:43:58.580 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/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
17:43:58.581 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
17:43:58.581 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:58.581 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.582 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
17:43:58.582 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.582 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.582 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.583 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
17:43:58.583 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.584 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.584 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.585 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.586 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
17:43:58.586 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.586 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.586 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.587 INFO  Funcotator - Initializing Funcotator Engine...
17:43:58.591 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:58.591 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator8463214774977887074.vcf
17:43:58.592 INFO  ProgressMeter - Starting traversal
17:43:58.592 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.598 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
17:43:58.601 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3011510272
17:43:58.655 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.658 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6990616751978970017.so: /tmp/libgkl_compression6990616751978970017.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.658 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.661 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9278681912816334781.so: /tmp/libgkl_compression9278681912816334781.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.662 INFO  Funcotator - ------------------------------------------------------------
17:43:58.662 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:58.662 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:58.662 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:58.662 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:58.662 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:58.662 INFO  Funcotator - ------------------------------------------------------------
17:43:58.662 INFO  Funcotator - ------------------------------------------------------------
17:43:58.662 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:58.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:58.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:58.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:58.662 INFO  Funcotator - Deflater: JdkDeflater
17:43:58.662 INFO  Funcotator - Inflater: JdkInflater
17:43:58.662 INFO  Funcotator - GCS max retries/reopens: 20
17:43:58.662 INFO  Funcotator - Requester pays: disabled
17:43:58.662 INFO  Funcotator - Initializing engine
17:43:58.664 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:58.665 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
17:43:58.666 INFO  Funcotator - Done initializing engine
17:43:58.666 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:58.666 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:58.666 INFO  Funcotator - Initializing data sources...
17:43:58.666 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
17:43:58.666 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:58.666 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
17:43:58.666 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
17:43:58.666 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
17:43:58.666 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:58.666 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
17:43:58.666 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
17:43:58.667 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
17:43:58.667 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
17:43:58.668 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
17:43:58.668 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
17:43:58.668 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:58.669 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
17:43:58.669 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
17:43:58.670 INFO  Funcotator - Initializing Funcotator Engine...
17:43:58.670 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:58.670 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.
17:43:58.670 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:58.670 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing2041710053720986873.vcf
17:43:58.670 INFO  ProgressMeter - Starting traversal
17:43:58.670 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.677 INFO  ProgressMeter -             unmapped              0.0                     1           8571.4
17:43:58.677 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:43:58.677 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
17:43:58.680 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:58.681 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing2041710053720986873.vcf
17:43:58.737 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.740 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17742825217077548760.so: /tmp/libgkl_compression17742825217077548760.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.740 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.742 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15282613262359218224.so: /tmp/libgkl_compression15282613262359218224.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.743 INFO  Funcotator - ------------------------------------------------------------
17:43:58.743 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:58.743 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:58.743 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:58.743 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:58.743 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:58.743 INFO  Funcotator - ------------------------------------------------------------
17:43:58.743 INFO  Funcotator - ------------------------------------------------------------
17:43:58.743 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:58.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:58.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:58.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:58.743 INFO  Funcotator - Deflater: JdkDeflater
17:43:58.744 INFO  Funcotator - Inflater: JdkInflater
17:43:58.744 INFO  Funcotator - GCS max retries/reopens: 20
17:43:58.744 INFO  Funcotator - Requester pays: disabled
17:43:58.744 INFO  Funcotator - Initializing engine
17:43:58.744 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
17:43:58.748 INFO  Funcotator - Done initializing engine
17:43:58.748 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:58.748 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:58.748 INFO  Funcotator - Initializing data sources...
17:43:58.748 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:58.748 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:58.748 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
17:43:58.748 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
17:43:58.748 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
17:43:58.748 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:58.748 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
17:43:58.749 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:58.749 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:58.749 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:58.750 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:58.750 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:58.750 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:58.751 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:58.753 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
17:43:58.753 INFO  Funcotator - Initializing Funcotator Engine...
17:43:58.754 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:58.754 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.
17:43:58.754 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15749792794931925494.maf
17:43:58.754 INFO  ProgressMeter - Starting traversal
17:43:58.754 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.757 WARN  MafOutputRenderer - 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=
17:43:58.757 WARN  MafOutputRenderer - 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=
17:43:58.758 WARN  MafOutputRenderer - 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=
17:43:58.758 WARN  MafOutputRenderer - 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=
17:43:58.759 WARN  MafOutputRenderer - 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=
17:43:58.759 WARN  MafOutputRenderer - 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=
17:43:58.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 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=
17:43:58.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 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=
17:43:58.761 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 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=
17:43:58.761 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 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=
17:43:58.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 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=
17:43:58.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 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=
17:43:58.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 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=
17:43:58.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 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=
17:43:58.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 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=
17:43:58.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 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=
17:43:58.764 WARN  MafOutputRenderer - 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=
17:43:58.764 WARN  MafOutputRenderer - 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=
17:43:58.764 WARN  MafOutputRenderer - 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=
17:43:58.765 WARN  MafOutputRenderer - 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=
17:43:58.765 WARN  MafOutputRenderer - 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=
17:43:58.765 INFO  ProgressMeter -             unmapped              0.0                    21         114545.5
17:43:58.765 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
17:43:58.765 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:43:58.765 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:58.768 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
17:43:58.770 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
17:43:58.827 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.830 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14634100949626430377.so: /tmp/libgkl_compression14634100949626430377.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.830 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.833 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11909847897197008363.so: /tmp/libgkl_compression11909847897197008363.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.834 INFO  Funcotator - ------------------------------------------------------------
17:43:58.834 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:58.834 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:58.834 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:58.834 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:58.834 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:58.834 INFO  Funcotator - ------------------------------------------------------------
17:43:58.834 INFO  Funcotator - ------------------------------------------------------------
17:43:58.834 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:58.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:58.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:58.834 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:58.834 INFO  Funcotator - Deflater: JdkDeflater
17:43:58.834 INFO  Funcotator - Inflater: JdkInflater
17:43:58.834 INFO  Funcotator - GCS max retries/reopens: 20
17:43:58.834 INFO  Funcotator - Requester pays: disabled
17:43:58.834 INFO  Funcotator - Initializing engine
17:43:58.835 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
17:43:58.837 INFO  Funcotator - Done initializing engine
17:43:58.837 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:58.837 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:58.837 INFO  Funcotator - Initializing data sources...
17:43:58.837 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:58.837 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:58.837 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
17:43:58.837 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
17:43:58.837 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
17:43:58.837 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:58.837 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
17:43:58.837 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:58.838 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
17:43:58.838 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
17:43:58.838 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
17:43:58.839 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:58.839 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
17:43:58.840 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
17:43:58.841 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
17:43:58.842 INFO  Funcotator - Initializing Funcotator Engine...
17:43:58.842 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:58.842 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.
17:43:58.842 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4733623930519837487.vcf
17:43:58.845 INFO  ProgressMeter - Starting traversal
17:43:58.846 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.855 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
17:43:58.855 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
17:43:58.855 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:43:58.858 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:58.859 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4733623930519837487.vcf
17:43:58.915 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.918 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12917727856381691504.so: /tmp/libgkl_compression12917727856381691504.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.918 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.921 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3407608220355808426.so: /tmp/libgkl_compression3407608220355808426.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.922 INFO  Funcotator - ------------------------------------------------------------
17:43:58.922 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:58.922 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:58.922 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:58.922 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:58.922 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:58.922 INFO  Funcotator - ------------------------------------------------------------
17:43:58.922 INFO  Funcotator - ------------------------------------------------------------
17:43:58.922 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:58.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:58.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:58.922 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:58.922 INFO  Funcotator - Deflater: JdkDeflater
17:43:58.922 INFO  Funcotator - Inflater: JdkInflater
17:43:58.922 INFO  Funcotator - GCS max retries/reopens: 20
17:43:58.922 INFO  Funcotator - Requester pays: disabled
17:43:58.922 INFO  Funcotator - Initializing engine
17:43:58.923 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
17:43:58.924 INFO  Funcotator - Done initializing engine
17:43:58.924 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:58.924 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:58.924 INFO  Funcotator - Initializing data sources...
17:43:58.924 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:58.924 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:58.924 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
17:43:58.924 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
17:43:58.924 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
17:43:58.924 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:58.924 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
17:43:58.924 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:58.925 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
17:43:58.925 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
17:43:58.926 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
17:43:58.926 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:58.926 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
17:43:58.927 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
17:43:58.928 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
17:43:58.929 INFO  Funcotator - Initializing Funcotator Engine...
17:43:58.929 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:58.929 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.
17:43:58.929 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:58.929 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11347266296722343082.vcf
17:43:58.930 INFO  ProgressMeter - Starting traversal
17:43:58.930 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:58.936 INFO  ProgressMeter -             unmapped              0.0                     5          50000.0
17:43:58.936 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
17:43:58.936 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:43:58.938 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:58 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:58.939 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11347266296722343082.vcf
17:43:58.996 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:58.998 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14579148353902927248.so: /tmp/libgkl_compression14579148353902927248.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:58.999 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.001 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression10210748357025294749.so: /tmp/libgkl_compression10210748357025294749.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.002 INFO  Funcotator - ------------------------------------------------------------
17:43:59.002 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:59.002 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:59.002 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:59.002 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:59.002 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:58 PM UTC
17:43:59.002 INFO  Funcotator - ------------------------------------------------------------
17:43:59.002 INFO  Funcotator - ------------------------------------------------------------
17:43:59.002 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:59.002 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:59.002 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:59.002 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:59.002 INFO  Funcotator - Deflater: JdkDeflater
17:43:59.002 INFO  Funcotator - Inflater: JdkInflater
17:43:59.002 INFO  Funcotator - GCS max retries/reopens: 20
17:43:59.002 INFO  Funcotator - Requester pays: disabled
17:43:59.002 INFO  Funcotator - Initializing engine
17:43:59.004 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
17:43:59.004 INFO  Funcotator - Done initializing engine
17:43:59.004 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:59.004 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:59.004 INFO  Funcotator - Initializing data sources...
17:43:59.004 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:59.004 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:59.005 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
17:43:59.005 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
17:43:59.005 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
17:43:59.005 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:59.005 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
17:43:59.005 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:59.006 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
17:43:59.006 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
17:43:59.006 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
17:43:59.006 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:59.007 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
17:43:59.008 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
17:43:59.009 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
17:43:59.010 INFO  Funcotator - Initializing Funcotator Engine...
17:43:59.010 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:59.010 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.
17:43:59.010 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:59.010 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17451638729834503815.vcf
17:43:59.011 INFO  ProgressMeter - Starting traversal
17:43:59.011 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:59.020 INFO  ProgressMeter -             unmapped              0.0                    15         100000.0
17:43:59.020 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
17:43:59.020 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
17:43:59.023 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:59.078 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.080 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression627680790395338570.so: /tmp/libgkl_compression627680790395338570.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.080 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.083 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12945200063715833418.so: /tmp/libgkl_compression12945200063715833418.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.084 INFO  Funcotator - ------------------------------------------------------------
17:43:59.084 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:59.084 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:59.084 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:59.084 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:59.084 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:59 PM UTC
17:43:59.084 INFO  Funcotator - ------------------------------------------------------------
17:43:59.084 INFO  Funcotator - ------------------------------------------------------------
17:43:59.084 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:59.084 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:59.084 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:59.084 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:59.084 INFO  Funcotator - Deflater: JdkDeflater
17:43:59.084 INFO  Funcotator - Inflater: JdkInflater
17:43:59.084 INFO  Funcotator - GCS max retries/reopens: 20
17:43:59.084 INFO  Funcotator - Requester pays: disabled
17:43:59.084 INFO  Funcotator - Initializing engine
17:43:59.085 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
17:43:59.086 INFO  Funcotator - Done initializing engine
17:43:59.086 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:59.086 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:59.086 INFO  Funcotator - Initializing data sources...
17:43:59.086 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:59.086 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:59.086 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
17:43:59.086 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
17:43:59.086 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
17:43:59.086 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:59.086 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
17:43:59.086 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:59.087 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
17:43:59.087 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
17:43:59.088 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
17:43:59.088 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:59.088 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
17:43:59.089 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
17:43:59.090 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
17:43:59.091 INFO  Funcotator - Initializing Funcotator Engine...
17:43:59.091 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:59.091 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.
17:43:59.091 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:59.091 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3802737570520359219.maf
17:43:59.091 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
17:43:59.092 INFO  ProgressMeter - Starting traversal
17:43:59.092 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:59.094 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
17:43:59.095 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.096 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.097 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.097 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
17:43:59.097 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
17:43:59.098 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.098 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
17:43:59.098 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.099 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
17:43:59.099 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
17:43:59.099 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
17:43:59.100 WARN  MafOutputRenderer - 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=
17:43:59.100 WARN  MafOutputRenderer - 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=
17:43:59.100 WARN  MafOutputRenderer - 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=
17:43:59.101 INFO  ProgressMeter -             unmapped              0.0                    15         100000.0
17:43:59.101 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
17:43:59.101 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
17:43:59.101 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:59.102 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17451638729834503815.vcf
17:43:59.160 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.162 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6080641542167186513.so: /tmp/libgkl_compression6080641542167186513.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.163 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.165 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15418549610672770373.so: /tmp/libgkl_compression15418549610672770373.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.166 INFO  Funcotator - ------------------------------------------------------------
17:43:59.166 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:59.166 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:59.166 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:59.166 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:59.166 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:59 PM UTC
17:43:59.166 INFO  Funcotator - ------------------------------------------------------------
17:43:59.166 INFO  Funcotator - ------------------------------------------------------------
17:43:59.166 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:59.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:59.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:59.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:59.166 INFO  Funcotator - Deflater: JdkDeflater
17:43:59.166 INFO  Funcotator - Inflater: JdkInflater
17:43:59.166 INFO  Funcotator - GCS max retries/reopens: 20
17:43:59.166 INFO  Funcotator - Requester pays: disabled
17:43:59.166 INFO  Funcotator - Initializing engine
17:43:59.168 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
17:43:59.168 INFO  Funcotator - Done initializing engine
17:43:59.168 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:59.168 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:59.168 INFO  Funcotator - Initializing data sources...
17:43:59.168 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:59.168 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:59.169 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
17:43:59.169 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
17:43:59.169 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
17:43:59.169 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:59.169 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
17:43:59.169 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:59.169 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
17:43:59.170 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
17:43:59.170 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
17:43:59.170 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:59.171 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
17:43:59.171 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
17:43:59.173 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
17:43:59.174 INFO  Funcotator - Initializing Funcotator Engine...
17:43:59.174 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:59.174 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.
17:43:59.174 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:59.174 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11926169060852706591.vcf
17:43:59.174 INFO  ProgressMeter - Starting traversal
17:43:59.174 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:59.210 INFO  ProgressMeter -             unmapped              0.0                    57          95000.0
17:43:59.210 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
17:43:59.210 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:59.213 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:59.269 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.272 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1678873747178728052.so: /tmp/libgkl_compression1678873747178728052.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.272 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.275 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9110900260604954998.so: /tmp/libgkl_compression9110900260604954998.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.276 INFO  Funcotator - ------------------------------------------------------------
17:43:59.276 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:59.276 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:59.276 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:59.276 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:59.276 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:59 PM UTC
17:43:59.276 INFO  Funcotator - ------------------------------------------------------------
17:43:59.276 INFO  Funcotator - ------------------------------------------------------------
17:43:59.276 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:59.276 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:59.276 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:59.276 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:59.276 INFO  Funcotator - Deflater: JdkDeflater
17:43:59.276 INFO  Funcotator - Inflater: JdkInflater
17:43:59.276 INFO  Funcotator - GCS max retries/reopens: 20
17:43:59.276 INFO  Funcotator - Requester pays: disabled
17:43:59.276 INFO  Funcotator - Initializing engine
17:43:59.277 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
17:43:59.278 INFO  Funcotator - Done initializing engine
17:43:59.278 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:59.278 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:59.278 INFO  Funcotator - Initializing data sources...
17:43:59.278 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:43:59.278 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:59.278 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:59.278 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
17:43:59.278 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
17:43:59.278 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:59.278 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:43:59.278 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:59.279 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
17:43:59.279 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:43:59.280 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:59.280 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:43:59.280 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
17:43:59.281 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:59.283 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:43:59.283 INFO  Funcotator - Initializing Funcotator Engine...
17:43:59.284 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:43:59.284 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.
17:43:59.284 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:59.284 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14822594534162969465.maf
17:43:59.284 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
17:43:59.284 INFO  ProgressMeter - Starting traversal
17:43:59.284 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:43:59.287 WARN  MafOutputRenderer - 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=
17:43:59.287 WARN  MafOutputRenderer - 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=
17:43:59.288 WARN  MafOutputRenderer - 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=
17:43:59.288 WARN  MafOutputRenderer - 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=
17:43:59.289 WARN  MafOutputRenderer - 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=
17:43:59.290 WARN  MafOutputRenderer - 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=
17:43:59.290 WARN  MafOutputRenderer - 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=
17:43:59.291 WARN  MafOutputRenderer - 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=
17:43:59.291 WARN  MafOutputRenderer - 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=
17:43:59.292 WARN  MafOutputRenderer - 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=
17:43:59.292 WARN  MafOutputRenderer - 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=
17:43:59.292 WARN  MafOutputRenderer - 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=
17:43:59.293 WARN  MafOutputRenderer - 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=
17:43:59.294 WARN  MafOutputRenderer - 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=
17:43:59.295 WARN  MafOutputRenderer - 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=
17:43:59.295 WARN  MafOutputRenderer - 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=
17:43:59.296 WARN  MafOutputRenderer - 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=
17:43:59.296 WARN  MafOutputRenderer - 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=
17:43:59.296 WARN  MafOutputRenderer - 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=
17:43:59.297 WARN  MafOutputRenderer - 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=
17:43:59.298 WARN  MafOutputRenderer - 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=
17:43:59.299 WARN  MafOutputRenderer - 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=
17:43:59.300 WARN  MafOutputRenderer - 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=
17:43:59.300 WARN  MafOutputRenderer - 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=
17:43:59.301 WARN  MafOutputRenderer - 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=
17:43:59.302 WARN  MafOutputRenderer - 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=
17:43:59.302 WARN  MafOutputRenderer - 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=
17:43:59.304 WARN  MafOutputRenderer - 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=
17:43:59.304 WARN  MafOutputRenderer - 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=
17:43:59.304 WARN  MafOutputRenderer - 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=
17:43:59.305 WARN  MafOutputRenderer - 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=
17:43:59.306 WARN  MafOutputRenderer - 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=
17:43:59.306 WARN  MafOutputRenderer - 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=
17:43:59.307 WARN  MafOutputRenderer - 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=
17:43:59.307 WARN  MafOutputRenderer - 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=
17:43:59.309 WARN  MafOutputRenderer - 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=
17:43:59.309 WARN  MafOutputRenderer - 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=
17:43:59.310 WARN  MafOutputRenderer - 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=
17:43:59.311 WARN  MafOutputRenderer - 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=
17:43:59.311 WARN  MafOutputRenderer - 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=
17:43:59.311 WARN  MafOutputRenderer - 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=
17:43:59.313 WARN  MafOutputRenderer - 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=
17:43:59.313 WARN  MafOutputRenderer - 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=
17:43:59.313 WARN  MafOutputRenderer - 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=
17:43:59.314 WARN  MafOutputRenderer - 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=
17:43:59.315 WARN  MafOutputRenderer - 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=
17:43:59.315 WARN  MafOutputRenderer - 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=
17:43:59.316 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 @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
17:43:59.316 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 @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
17:43:59.317 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 @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
17:43:59.318 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 @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
17:43:59.318 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 @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
17:43:59.319 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 @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
17:43:59.320 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 @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
17:43:59.320 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 @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
17:43:59.321 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 @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
17:43:59.321 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 @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
17:43:59.321 INFO  ProgressMeter -             unmapped              0.0                    57          92432.4
17:43:59.321 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
17:43:59.321 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:43:59.321 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:43:59 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3011510272
17:43:59.322 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11926169060852706591.vcf
17:43:59.383 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.386 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9421933747477201296.so: /tmp/libgkl_compression9421933747477201296.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.386 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:43:59.389 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression12005917109572326300.so: /tmp/libgkl_compression12005917109572326300.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:43:59.390 INFO  Funcotator - ------------------------------------------------------------
17:43:59.390 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:43:59.390 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:43:59.390 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:43:59.390 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:43:59.390 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:43:59 PM UTC
17:43:59.390 INFO  Funcotator - ------------------------------------------------------------
17:43:59.390 INFO  Funcotator - ------------------------------------------------------------
17:43:59.390 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:43:59.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:43:59.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:43:59.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:43:59.390 INFO  Funcotator - Deflater: JdkDeflater
17:43:59.390 INFO  Funcotator - Inflater: JdkInflater
17:43:59.390 INFO  Funcotator - GCS max retries/reopens: 20
17:43:59.390 INFO  Funcotator - Requester pays: disabled
17:43:59.390 INFO  Funcotator - Initializing engine
17:43:59.391 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
17:43:59.392 INFO  Funcotator - Done initializing engine
17:43:59.392 INFO  Funcotator - Skipping sequence dictionary validation.
17:43:59.392 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:43:59.392 INFO  Funcotator - Initializing data sources...
17:43:59.392 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:43:59.392 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:43:59.392 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:59.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:59.394 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:43:59.394 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/hgnc_download_Nov302017.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
17:43:59.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:43:59.440 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:43:59.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:43:59.469 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:43:59.469 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:43:59.470 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/hg19/cosmic_fusion.tsv
17:43:59.470 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:43:59.470 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:43:59.471 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
17:43:59.471 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:43:59.579 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xrefseq_v75_37.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
17:43:59.592 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:43:59.759 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:43:59.759 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:59.760 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
17:43:59.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:43:59.799 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-10-27 17:43:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:43:59.800 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:43:59.800 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:43:59.801 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:59.801 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:43:59.801 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.802 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:59.802 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.802 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.803 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.804 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:59.804 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.804 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.805 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.806 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.807 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:43:59.807 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.807 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.808 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:43:59.809 INFO  Funcotator - Initializing Funcotator Engine...
17:43:59.809 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:43:59.809 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:43:59.810 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3813570184364579622.vcf
17:43:59.810 INFO  ProgressMeter - Starting traversal
17:43:59.810 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:14.631 INFO  ProgressMeter -        chr19:9077246              0.2                  1000           4048.3
17:44:25.305 INFO  ProgressMeter -        chr19:9077594              0.4                  2000           4706.8
17:44:26.125 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)
17:44:26.127 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)
17:44:27.448 INFO  ProgressMeter -        chr19:9077594              0.5                  2057           4465.6
17:44:27.448 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.5 minutes.
17:44:27.448 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
17:44:27.450 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:27 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.47 minutes.
Runtime.totalMemory()=3011510272
17:44:27.505 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:27.508 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7571432635089121234.so: /tmp/libgkl_compression7571432635089121234.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:27.508 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:27.511 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3439403904836871887.so: /tmp/libgkl_compression3439403904836871887.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:27.512 INFO  Funcotator - ------------------------------------------------------------
17:44:27.512 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:27.512 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:27.512 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:27.512 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:27.512 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:27 PM UTC
17:44:27.512 INFO  Funcotator - ------------------------------------------------------------
17:44:27.512 INFO  Funcotator - ------------------------------------------------------------
17:44:27.512 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:27.512 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:27.512 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:27.512 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:27.512 INFO  Funcotator - Deflater: JdkDeflater
17:44:27.512 INFO  Funcotator - Inflater: JdkInflater
17:44:27.512 INFO  Funcotator - GCS max retries/reopens: 20
17:44:27.512 INFO  Funcotator - Requester pays: disabled
17:44:27.512 INFO  Funcotator - Initializing engine
17:44:27.513 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
17:44:27.513 INFO  Funcotator - Done initializing engine
17:44:27.513 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:27.513 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:27.513 INFO  Funcotator - Initializing data sources...
17:44:27.513 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/
17:44:27.514 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:27.514 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
17:44:27.514 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
17:44:27.514 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
17:44:27.514 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
17:44:27.514 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
17:44:27.515 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:44:27.515 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:44:27.515 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
17:44:27.515 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
17:44:27.515 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
17:44:27.515 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:44:27.515 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
17:44:27.515 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
17:44:27.515 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
17:44:27.516 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
17:44:27.516 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:27.516 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
17:44:27.561 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CosmicTest.db -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
17:44:27.562 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/simple_uniprot_Dec012014.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
17:44:27.583 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_tissue.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
17:44:27.590 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:44:27.591 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dnaRepairGenes.20171221T103938.csv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
17:44:27.591 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/cosmic_fusion.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
17:44:27.591 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
17:44:27.591 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:27.592 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
17:44:27.593 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
17:44:27.668 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
17:44:27.681 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
17:44:27.875 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:44:27.875 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:44:27.876 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
17:44:27.914 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
17:44:27.914 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/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	2025-10-27 17:44:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:44:27.914 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/achilles_lineage_results.import.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
17:44:27.915 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:44:27.915 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:44:27.915 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
17:44:27.915 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.916 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:44:27.916 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.916 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.918 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.918 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:44:27.919 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.919 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.920 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.921 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.922 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
17:44:27.922 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.922 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.923 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:44:27.924 INFO  Funcotator - Initializing Funcotator Engine...
17:44:27.924 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:44:27.924 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:44:27.924 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1255487937601541448.maf
17:44:27.924 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
17:44:27.925 INFO  ProgressMeter - Starting traversal
17:44:27.925 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:42.795 INFO  ProgressMeter -        chr19:9077246              0.2                  1000           4035.0
17:44:53.611 INFO  ProgressMeter -        chr19:9077594              0.4                  2000           4671.8
17:44:54.442 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)
17:44:54.443 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)
17:44:55.783 INFO  ProgressMeter -        chr19:9077594              0.5                  2057           4430.3
17:44:55.783 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.5 minutes.
17:44:55.784 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
17:44:55.784 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:55 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.47 minutes.
Runtime.totalMemory()=3128950784
17:44:55.785 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3813570184364579622.vcf
17:44:56.152 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.155 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1676421745421142115.so: /tmp/libgkl_compression1676421745421142115.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.155 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.158 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13766162385151375948.so: /tmp/libgkl_compression13766162385151375948.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.159 INFO  Funcotator - ------------------------------------------------------------
17:44:56.159 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.159 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.159 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.159 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.159 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.159 INFO  Funcotator - ------------------------------------------------------------
17:44:56.159 INFO  Funcotator - ------------------------------------------------------------
17:44:56.159 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.159 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.159 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.159 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.159 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.159 INFO  Funcotator - Inflater: JdkInflater
17:44:56.159 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.159 INFO  Funcotator - Requester pays: disabled
17:44:56.160 INFO  Funcotator - Initializing engine
17:44:56.161 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
17:44:56.184 INFO  Funcotator - Done initializing engine
17:44:56.185 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.185 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.185 INFO  Funcotator - Initializing data sources...
17:44:56.185 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:44:56.185 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.185 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
17:44:56.185 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
17:44:56.185 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
17:44:56.185 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.185 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
17:44:56.185 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.186 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
17:44:56.186 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
17:44:56.187 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
17:44:56.187 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:44:56.187 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
17:44:56.195 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
17:44:56.204 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
17:44:56.212 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.218 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:44:56.218 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15252096946799996658.vcf
17:44:56.230 INFO  ProgressMeter - Starting traversal
17:44:56.230 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.257 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
17:44:56.257 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
17:44:56.257 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:44:56.263 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.320 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.323 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8091429108017253122.so: /tmp/libgkl_compression8091429108017253122.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.323 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.326 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2051593614508965020.so: /tmp/libgkl_compression2051593614508965020.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.327 INFO  Funcotator - ------------------------------------------------------------
17:44:56.327 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.327 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.327 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.327 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.327 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.327 INFO  Funcotator - ------------------------------------------------------------
17:44:56.327 INFO  Funcotator - ------------------------------------------------------------
17:44:56.327 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.327 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.327 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.327 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.327 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.327 INFO  Funcotator - Inflater: JdkInflater
17:44:56.327 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.327 INFO  Funcotator - Requester pays: disabled
17:44:56.327 INFO  Funcotator - Initializing engine
17:44:56.328 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
17:44:56.352 INFO  Funcotator - Done initializing engine
17:44:56.352 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.352 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.352 INFO  Funcotator - Initializing data sources...
17:44:56.352 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:44:56.352 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.352 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
17:44:56.352 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
17:44:56.353 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
17:44:56.353 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.353 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
17:44:56.353 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.354 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
17:44:56.354 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
17:44:56.354 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
17:44:56.354 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:44:56.355 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
17:44:56.363 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
17:44:56.372 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
17:44:56.380 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.386 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:44:56.386 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out2316712966428802725.maf
17:44:56.387 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
17:44:56.387 INFO  ProgressMeter - Starting traversal
17:44:56.387 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.390 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 @ 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=
17:44:56.394 WARN  MafOutputRenderer - 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=
17:44:56.394 WARN  MafOutputRenderer - 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+
17:44:56.395 WARN  MafOutputRenderer - 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+
17:44:56.395 WARN  MafOutputRenderer - 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+
17:44:56.395 WARN  MafOutputRenderer - 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+
17:44:56.395 WARN  MafOutputRenderer - 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=
17:44:56.396 WARN  MafOutputRenderer - 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=
17:44:56.396 WARN  MafOutputRenderer - 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=
17:44:56.396 WARN  MafOutputRenderer - 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=
17:44:56.396 WARN  MafOutputRenderer - 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=
17:44:56.397 WARN  MafOutputRenderer - 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=
17:44:56.397 WARN  MafOutputRenderer - 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=
17:44:56.397 WARN  MafOutputRenderer - 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=
17:44:56.398 WARN  MafOutputRenderer - 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=
17:44:56.398 WARN  MafOutputRenderer - 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=
17:44:56.398 WARN  MafOutputRenderer - 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=
17:44:56.398 WARN  MafOutputRenderer - 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=
17:44:56.399 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179172828 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=
17:44:56.399 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173402 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+
17:44:56.399 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173404 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
17:44:56.400 WARN  MafOutputRenderer - 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=
17:44:56.400 WARN  MafOutputRenderer - 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=
17:44:56.400 WARN  MafOutputRenderer - 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=
17:44:56.401 WARN  MafOutputRenderer - 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=
17:44:56.401 WARN  MafOutputRenderer - 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=
17:44:56.401 WARN  MafOutputRenderer - 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=
17:44:56.401 WARN  MafOutputRenderer - 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=
17:44:56.402 WARN  MafOutputRenderer - 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
17:44:56.402 WARN  MafOutputRenderer - 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=
17:44:56.402 WARN  MafOutputRenderer - 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=
17:44:56.403 WARN  MafOutputRenderer - 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=
17:44:56.403 WARN  MafOutputRenderer - 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=
17:44:56.403 WARN  MafOutputRenderer - 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=
17:44:56.403 WARN  MafOutputRenderer - 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=
17:44:56.404 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215575 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=
17:44:56.404 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179217522 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=
17:44:56.404 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221303 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=
17:44:56.404 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221696 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=
17:44:56.405 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179224643 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=
17:44:56.405 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179226199 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=
17:44:56.406 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179231630 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=
17:44:56.406 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232352 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=
17:44:56.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232509 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=
17:44:56.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179236244-179236250 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=
17:44:56.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179242400-179242401 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=
17:44:56.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179243192 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+
17:44:56.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244582 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=
17:44:56.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244703 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=
17:44:56.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179246281 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=
17:44:56.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179247445 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=
17:44:56.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249007 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=
17:44:56.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249792 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=
17:44:56.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249918 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=
17:44:56.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250038 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=
17:44:56.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250846 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=
17:44:56.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250872 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=
17:44:56.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251319 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=
17:44:56.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251568-179251569 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=
17:44:56.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251754 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=
17:44:56.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251923 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=
17:44:56.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251953 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=
17:44:56.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179252222 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=
17:44:56.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253641 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=
17:44:56.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253762 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=
17:44:56.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255161 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=
17:44:56.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255164 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=
17:44:56.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255188 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=
17:44:56.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255255 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=
17:44:56.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255327 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=
17:44:56.413 WARN  MafOutputRenderer - 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=
17:44:56.413 WARN  MafOutputRenderer - 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=
17:44:56.413 WARN  MafOutputRenderer - 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=
17:44:56.413 WARN  MafOutputRenderer - 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=
17:44:56.413 WARN  MafOutputRenderer - 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=
17:44:56.414 WARN  MafOutputRenderer - 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=
17:44:56.414 WARN  MafOutputRenderer - 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=
17:44:56.414 WARN  MafOutputRenderer - 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=
17:44:56.414 WARN  MafOutputRenderer - 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=
17:44:56.414 WARN  MafOutputRenderer - 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=
17:44:56.415 WARN  MafOutputRenderer - 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=
17:44:56.415 WARN  MafOutputRenderer - 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=
17:44:56.415 WARN  MafOutputRenderer - 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=
17:44:56.415 WARN  MafOutputRenderer - 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=
17:44:56.416 WARN  MafOutputRenderer - 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=
17:44:56.416 WARN  MafOutputRenderer - 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=
17:44:56.416 WARN  MafOutputRenderer - 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=
17:44:56.416 WARN  MafOutputRenderer - 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=
17:44:56.416 WARN  MafOutputRenderer - 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=
17:44:56.417 WARN  MafOutputRenderer - 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=
17:44:56.417 WARN  MafOutputRenderer - 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=
17:44:56.417 WARN  MafOutputRenderer - 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=
17:44:56.417 WARN  MafOutputRenderer - 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=
17:44:56.417 WARN  MafOutputRenderer - 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=
17:44:56.418 WARN  MafOutputRenderer - 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=
17:44:56.418 WARN  MafOutputRenderer - 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=
17:44:56.418 WARN  MafOutputRenderer - 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=
17:44:56.418 WARN  MafOutputRenderer - 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=
17:44:56.418 WARN  MafOutputRenderer - 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=
17:44:56.419 WARN  MafOutputRenderer - 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=
17:44:56.419 INFO  ProgressMeter -             unmapped              0.0                   100         187500.0
17:44:56.419 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
17:44:56.419 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:44:56.419 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.420 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15252096946799996658.vcf
17:44:56.547 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.550 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7253227142968150395.so: /tmp/libgkl_compression7253227142968150395.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.550 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.553 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4436553286161743250.so: /tmp/libgkl_compression4436553286161743250.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.554 INFO  Funcotator - ------------------------------------------------------------
17:44:56.554 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.554 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.554 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.554 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.554 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.554 INFO  Funcotator - ------------------------------------------------------------
17:44:56.554 INFO  Funcotator - ------------------------------------------------------------
17:44:56.554 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.554 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.554 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.554 INFO  Funcotator - Inflater: JdkInflater
17:44:56.554 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.554 INFO  Funcotator - Requester pays: disabled
17:44:56.554 INFO  Funcotator - Initializing engine
17:44:56.555 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
17:44:56.555 INFO  Funcotator - Done initializing engine
17:44:56.555 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.555 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.556 INFO  Funcotator - Initializing data sources...
17:44:56.556 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:44:56.556 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.556 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
17:44:56.556 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
17:44:56.556 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
17:44:56.556 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.556 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
17:44:56.556 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.557 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
17:44:56.557 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
17:44:56.557 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
17:44:56.557 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:44:56.558 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
17:44:56.559 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
17:44:56.560 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
17:44:56.561 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.561 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:44:56.561 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.
17:44:56.561 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:44:56.561 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7829679596709581304.vcf
17:44:56.562 INFO  ProgressMeter - Starting traversal
17:44:56.562 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.597 INFO  ProgressMeter -             unmapped              0.0                    57          97714.3
17:44:56.597 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
17:44:56.597 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:44:56.600 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.655 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.658 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13190033070641639163.so: /tmp/libgkl_compression13190033070641639163.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.658 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.661 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4369691305096218982.so: /tmp/libgkl_compression4369691305096218982.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.662 INFO  Funcotator - ------------------------------------------------------------
17:44:56.662 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.662 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.662 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.662 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.662 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.662 INFO  Funcotator - ------------------------------------------------------------
17:44:56.662 INFO  Funcotator - ------------------------------------------------------------
17:44:56.662 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.662 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.662 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.662 INFO  Funcotator - Inflater: JdkInflater
17:44:56.662 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.662 INFO  Funcotator - Requester pays: disabled
17:44:56.662 INFO  Funcotator - Initializing engine
17:44:56.663 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
17:44:56.664 INFO  Funcotator - Done initializing engine
17:44:56.664 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.664 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.664 INFO  Funcotator - Initializing data sources...
17:44:56.664 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:44:56.664 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.664 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
17:44:56.664 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
17:44:56.664 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
17:44:56.664 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.664 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
17:44:56.664 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.665 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
17:44:56.665 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
17:44:56.666 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
17:44:56.666 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:44:56.666 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
17:44:56.667 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
17:44:56.669 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
17:44:56.670 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.670 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:44:56.670 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.
17:44:56.670 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
17:44:56.670 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out820840237723038024.maf
17:44:56.670 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
17:44:56.670 INFO  ProgressMeter - Starting traversal
17:44:56.670 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.673 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
17:44:56.673 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
17:44:56.673 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 @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
17:44:56.674 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 @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
17:44:56.675 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
17:44:56.675 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
17:44:56.676 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 @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
17:44:56.677 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 @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
17:44:56.677 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 @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
17:44:56.677 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 @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
17:44:56.678 WARN  MafOutputRenderer - 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=
17:44:56.678 WARN  MafOutputRenderer - 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=
17:44:56.678 WARN  MafOutputRenderer - 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=
17:44:56.680 WARN  MafOutputRenderer - 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=
17:44:56.680 WARN  MafOutputRenderer - 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=
17:44:56.681 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
17:44:56.681 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
17:44:56.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
17:44:56.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
17:44:56.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
17:44:56.684 WARN  MafOutputRenderer - 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=
17:44:56.684 WARN  MafOutputRenderer - 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=
17:44:56.685 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
17:44:56.686 WARN  MafOutputRenderer - 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=
17:44:56.686 WARN  MafOutputRenderer - 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=
17:44:56.687 WARN  MafOutputRenderer - 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=
17:44:56.688 WARN  MafOutputRenderer - 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=
17:44:56.689 WARN  MafOutputRenderer - 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=
17:44:56.689 WARN  MafOutputRenderer - 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=
17:44:56.690 WARN  MafOutputRenderer - 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=
17:44:56.690 WARN  MafOutputRenderer - 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=
17:44:56.691 WARN  MafOutputRenderer - 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=
17:44:56.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
17:44:56.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
17:44:56.693 WARN  MafOutputRenderer - 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=
17:44:56.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
17:44:56.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
17:44:56.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
17:44:56.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
17:44:56.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
17:44:56.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
17:44:56.698 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
17:44:56.698 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
17:44:56.701 WARN  MafOutputRenderer - 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=
17:44:56.702 WARN  MafOutputRenderer - 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=
17:44:56.703 WARN  MafOutputRenderer - 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=
17:44:56.703 WARN  MafOutputRenderer - 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=
17:44:56.704 WARN  MafOutputRenderer - 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=
17:44:56.704 WARN  MafOutputRenderer - 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=
17:44:56.705 WARN  MafOutputRenderer - 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=
17:44:56.706 WARN  MafOutputRenderer - 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=
17:44:56.706 WARN  MafOutputRenderer - 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=
17:44:56.706 WARN  MafOutputRenderer - 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=
17:44:56.708 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
17:44:56.708 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
17:44:56.708 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
17:44:56.709 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
17:44:56.709 INFO  ProgressMeter -             unmapped              0.0                    57          87692.3
17:44:56.709 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
17:44:56.709 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
17:44:56.709 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.710 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7829679596709581304.vcf
17:44:56.796 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.799 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1200891017295334732.so: /tmp/libgkl_compression1200891017295334732.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.799 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.802 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1373991865868421292.so: /tmp/libgkl_compression1373991865868421292.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.803 INFO  Funcotator - ------------------------------------------------------------
17:44:56.803 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.803 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.803 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.803 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.803 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.803 INFO  Funcotator - ------------------------------------------------------------
17:44:56.803 INFO  Funcotator - ------------------------------------------------------------
17:44:56.803 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.803 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.803 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.803 INFO  Funcotator - Inflater: JdkInflater
17:44:56.803 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.803 INFO  Funcotator - Requester pays: disabled
17:44:56.803 INFO  Funcotator - Initializing engine
17:44:56.804 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
17:44:56.805 INFO  Funcotator - Done initializing engine
17:44:56.805 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.805 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.805 INFO  Funcotator - Initializing data sources...
17:44:56.805 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/
17:44:56.806 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.806 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:44:56.806 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:44:56.806 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:44:56.806 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.806 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA.gtf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:44:56.806 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.807 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:44:56.807 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/gencode.v19.PIK3CA_transcript.fasta -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
17:44:56.807 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
17:44:56.807 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
17:44:56.808 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:44:56.809 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/dummy_clinvar_hg19_pik3ca.vcf -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:44:56.810 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
17:44:56.811 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.811 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:44:56.811 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
17:44:56.811 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15028770770860423888.maf
17:44:56.812 INFO  ProgressMeter - Starting traversal
17:44:56.812 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.814 WARN  MafOutputRenderer - 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=
17:44:56.815 WARN  MafOutputRenderer - 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=
17:44:56.816 WARN  MafOutputRenderer - 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=
17:44:56.816 WARN  MafOutputRenderer - 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=
17:44:56.817 WARN  MafOutputRenderer - 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=
17:44:56.817 WARN  MafOutputRenderer - 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=
17:44:56.818 WARN  MafOutputRenderer - 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=
17:44:56.818 WARN  MafOutputRenderer - 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=
17:44:56.818 WARN  MafOutputRenderer - 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=
17:44:56.819 WARN  MafOutputRenderer - 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=
17:44:56.819 WARN  MafOutputRenderer - 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=
17:44:56.820 WARN  MafOutputRenderer - 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=
17:44:56.820 WARN  MafOutputRenderer - 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=
17:44:56.820 WARN  MafOutputRenderer - 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=
17:44:56.821 WARN  MafOutputRenderer - 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=
17:44:56.821 WARN  MafOutputRenderer - 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=
17:44:56.821 WARN  MafOutputRenderer - 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=
17:44:56.822 WARN  MafOutputRenderer - 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=
17:44:56.822 WARN  MafOutputRenderer - 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=
17:44:56.822 WARN  MafOutputRenderer - 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=
17:44:56.823 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
17:44:56.823 INFO  ProgressMeter -             unmapped              0.0                    21         114545.5
17:44:56.823 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
17:44:56.823 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
17:44:56.823 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.882 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.885 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression16523040330701007884.so: /tmp/libgkl_compression16523040330701007884.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.885 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:56.888 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2008050003218230680.so: /tmp/libgkl_compression2008050003218230680.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:56.889 INFO  Funcotator - ------------------------------------------------------------
17:44:56.889 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:56.889 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:56.889 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:56.889 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:56.889 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:56 PM UTC
17:44:56.889 INFO  Funcotator - ------------------------------------------------------------
17:44:56.889 INFO  Funcotator - ------------------------------------------------------------
17:44:56.889 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:56.889 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:56.889 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:56.889 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:56.889 INFO  Funcotator - Deflater: JdkDeflater
17:44:56.889 INFO  Funcotator - Inflater: JdkInflater
17:44:56.889 INFO  Funcotator - GCS max retries/reopens: 20
17:44:56.889 INFO  Funcotator - Requester pays: disabled
17:44:56.889 INFO  Funcotator - Initializing engine
17:44:56.890 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
17:44:56.891 INFO  Funcotator - Done initializing engine
17:44:56.891 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:56.891 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:56.891 INFO  Funcotator - Initializing data sources...
17:44:56.891 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
17:44:56.891 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:56.892 INFO  DataSourceUtils - Resolved 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
17:44:56.892 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
17:44:56.892 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
17:44:56.892 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:56.892 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:44:56.892 INFO  DataSourceUtils - Resolved 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
17:44:56.893 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
17:44:56.932 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
17:44:56.933 INFO  DataSourceUtils - Resolved 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	2025-10-27 17:44:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:44:56.933 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_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
17:44:56.933 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:56.934 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
17:44:56.934 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
17:44:56.935 INFO  Funcotator - Initializing Funcotator Engine...
17:44:56.935 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:44:56.935 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.
17:44:56.935 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8113367487978584619.vcf
17:44:56.938 INFO  ProgressMeter - Starting traversal
17:44:56.938 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:56.942 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
17:44:56.942 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
17:44:56.942 WARN  Funcotator - ================================================================================
17:44:56.942 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:44:56.942 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:44:56.943 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:44:56.943 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:44:56.943 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:44:56.943 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:44:56.943 WARN  Funcotator - --------------------------------------------------------------------------------
17:44:56.943 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:44:56.943 WARN  Funcotator -  run was misconfigured.     
17:44:56.943 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:44:56.943 WARN  Funcotator - ================================================================================
17:44:56.943 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:56 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:56.944 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8113367487978584619.vcf
17:44:57.003 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:57.006 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression694400887026785668.so: /tmp/libgkl_compression694400887026785668.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:57.006 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:44:57.009 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3863017342185581943.so: /tmp/libgkl_compression3863017342185581943.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:44:57.010 INFO  Funcotator - ------------------------------------------------------------
17:44:57.010 INFO  Funcotator - org.broadinstitute.hellbender.tools.funcotator vUnavailable
17:44:57.010 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:44:57.010 INFO  Funcotator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:44:57.010 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:44:57.010 INFO  Funcotator - Start Date/Time: October 27, 2025 at 5:44:57 PM UTC
17:44:57.010 INFO  Funcotator - ------------------------------------------------------------
17:44:57.010 INFO  Funcotator - ------------------------------------------------------------
17:44:57.010 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:44:57.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:44:57.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:44:57.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:44:57.010 INFO  Funcotator - Deflater: JdkDeflater
17:44:57.010 INFO  Funcotator - Inflater: JdkInflater
17:44:57.010 INFO  Funcotator - GCS max retries/reopens: 20
17:44:57.010 INFO  Funcotator - Requester pays: disabled
17:44:57.010 INFO  Funcotator - Initializing engine
17:44:57.011 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
17:44:57.013 INFO  Funcotator - Done initializing engine
17:44:57.013 INFO  Funcotator - Skipping sequence dictionary validation.
17:44:57.013 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:44:57.013 INFO  Funcotator - Initializing data sources...
17:44:57.013 INFO  DataSourceUtils - Initializing data sources from directory: /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
17:44:57.013 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
17:44:57.013 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
17:44:57.013 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
17:44:57.013 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
17:44:57.013 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:44:57.013 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
17:44:57.014 INFO  DataSourceUtils - Resolved data source file path: file:///home/runner/work/gatk/gatk/clinvar_hgmd.tsv -> file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
17:44:57.014 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
17:44:57.055 INFO  DataSourceUtils - Resolved 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
17:44:57.056 INFO  DataSourceUtils - Resolved 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	2025-10-27 17:44:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
17:44:57.056 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
17:44:57.056 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:44:57.057 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
17:44:57.057 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
17:44:57.058 INFO  Funcotator - Initializing Funcotator Engine...
17:44:57.058 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
17:44:57.058 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.
17:44:57.058 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out981137109256480978.vcf
17:44:57.061 INFO  ProgressMeter - Starting traversal
17:44:57.061 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:44:57.063 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
17:44:57.063 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
17:44:57.063 WARN  Funcotator - ================================================================================
17:44:57.063 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
17:44:57.063 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
17:44:57.063 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
17:44:57.063 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
17:44:57.063 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
17:44:57.063 WARN  Funcotator -                                                   |___/                         ?[0;0m
17:44:57.063 WARN  Funcotator - --------------------------------------------------------------------------------
17:44:57.063 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
17:44:57.063 WARN  Funcotator -  run was misconfigured.     
17:44:57.063 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
17:44:57.063 WARN  Funcotator - ================================================================================
17:44:57.064 INFO  Funcotator - Shutting down engine
[October 27, 2025 at 5:44:57 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
17:44:57.065 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out981137109256480978.vcf