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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorIntegrationTest
58

tests
0

failures
0

ignored
1m43.22s

duration
100%

successful

Tests

Test Duration Result
exhaustiveArgumentTest[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.229s passed
exhaustiveArgumentTest[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.271s passed
exhaustiveArgumentTest[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 1.094s passed
exhaustiveArgumentTest[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.287s passed
exhaustiveArgumentTest[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.103s passed
exhaustiveArgumentTest[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.187s passed
exhaustiveArgumentTest[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.186s passed
exhaustiveArgumentTest[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.068s passed
metaTestEnsureTempDirs 0s passed
nonTrivialLargeDataValidationTest[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, [], false) 6.302s passed
nonTrivialLargeDataValidationTest[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf, [], false) 5.790s passed
nonTrivialLargeDataValidationTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false) 1.816s passed
nonTrivialLargeDataValidationTest[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, hg38, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf, [], false) 1.907s passed
nonTrivialLargeDataValidationTest[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf, [], true) 12.706s passed
testAlreadyAnnotatedInputWithOverrideArgument[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf) 5.889s passed
testAlreadyAnnotatedInputWithoutOverrideArgument[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf) 0.101s passed
testCanAnnotateHg38ClinvarAndGencodeV28 0.218s passed
testCanAnnotateMixedContigHg19Clinvar 0.123s passed
testCanAnnotateSpanningDeletions 0.195s passed
testCanCreateNonLocatableFuncotations 1.042s passed
testCanHandleSymbollicAlleleFuncotations 1.112s passed
testCustomVariantClassificationOrder 1.103s passed
testEColiFuncotations 0.177s passed
testEnsureDbSnpInMaf 0.105s passed
testExclusionFromDatasourceVcfToVcf 0.274s passed
testFilterParsing 0.152s passed
testFuncotatorWithoutValidatingResults[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.042s passed
testFuncotatorWithoutValidatingResults[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.153s passed
testFuncotatorWithoutValidatingResults[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 0.987s passed
testFuncotatorWithoutValidatingResults[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.080s passed
testFuncotatorWithoutValidatingResults[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.087s passed
testFuncotatorWithoutValidatingResults[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.039s passed
testFuncotatorWithoutValidatingResults[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder15348438429438650661/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 0.933s passed
testFuncotatorWithoutValidatingResults[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.035s passed
testMANESelectAnnotationDifferencesAndGencodeV43 0.376s passed
testMafCustomCountFieldsTumorOnly[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf) 0.109s passed
testMafCustomCountFieldsTumorOnly[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf) 0.104s passed
testMafCustomCountFields[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf) 0.103s passed
testMafCustomCountFields[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf) 0.101s passed
testManualAnnotationsCorrectness 0.123s passed
testMoreThanOneTNPair 0.098s passed
testNoSpanningDeletionWriteWithMAF 0.160s passed
testNoVariantsProduceMaf 0.095s passed
testSequenceDictionaryCheck 0.093s passed
testUnannotatedInputWithOverrideArgument[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf) 5.815s passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput 0.914s passed
testVCFColumnsArentShuffled 0.105s passed
testVCFToMAFPreservesFields 0.115s passed
testVCFToVCFPreservesFields 0.136s passed
testVcfDatasourceAccountsForAltAlleles 0.102s passed
testVcfMafConcordance[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder2481634388973871652/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15) 0.217s passed
testVcfMafConcordance[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder2481634388973871652/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.289s passed
testVcfMafConcordance[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder483318835674832473/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057) 36.254s passed
testVcfMafConcordance[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder5200219525200353651/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], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, false, 104) 0.424s passed
testVcfMafConcordance[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder2481634388973871652/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], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.293s passed
testVcfToMafHonorsExcludedFields 0.117s passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified 0.132s passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations 0.153s passed

Standard error

14:30:53.568 INFO  Funcotator - ------------------------------------------------------------
14:30:53.568 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:53.568 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:53.568 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:53.568 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:53.568 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:53 PM GMT
14:30:53.568 INFO  Funcotator - ------------------------------------------------------------
14:30:53.568 INFO  Funcotator - ------------------------------------------------------------
14:30:53.568 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:53.568 INFO  Funcotator - Picard Version: 3.4.0
14:30:53.568 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:53.568 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:53.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:53.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:53.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:53.568 INFO  Funcotator - Deflater: IntelDeflater
14:30:53.569 INFO  Funcotator - Inflater: IntelInflater
14:30:53.569 INFO  Funcotator - GCS max retries/reopens: 20
14:30:53.569 INFO  Funcotator - Requester pays: disabled
14:30:53.569 INFO  Funcotator - Initializing engine
14:30:53.570 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:30:53.571 INFO  Funcotator - Done initializing engine
14:30:53.571 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:53.571 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:53.571 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6855265211154251130/TranscriptIdFile.txt
14:30:53.571 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:30:53.571 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:53.571 INFO  Funcotator - Initializing data sources...
14:30:53.572 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:53.572 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:53.572 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:53.572 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:53.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:53.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:53.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:53.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:53.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:53.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:53.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:53.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:53.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:53.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:53.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:53.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:53.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:53.575 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:53.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:53.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:53.595 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:53.595 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:53.650 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:53.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:54.250 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:54.250 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:30:54.256 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:54.258 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:54.261 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:54.263 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:30:54.264 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:54.264 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:30:54.292 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:54.292 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:30:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:30:54.293 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:54.332 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:54.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:54.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:54.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:54.488 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:54.488 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:30:54.489 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:54.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:54.586 INFO  Funcotator - Initializing Funcotator Engine...
14:30:54.586 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:30:54.587 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:30:54.587 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:30:54.587 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:30:54.587 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:30:54.588 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:30:54.589 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:30:54.590 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:30:54.590 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:30:54.590 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.316984458754866940064.vcf
14:30:54.591 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:30:54.595 INFO  ProgressMeter - Starting traversal
14:30:54.595 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:30:54.704 INFO  ProgressMeter -             unmapped              0.0                     3           1651.4
14:30:54.704 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:30:54.704 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:30:54.708 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:30:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1797259264
14:30:54.830 INFO  Funcotator - ------------------------------------------------------------
14:30:54.830 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:54.830 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:54.830 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:54.830 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:54.831 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:54 PM GMT
14:30:54.831 INFO  Funcotator - ------------------------------------------------------------
14:30:54.831 INFO  Funcotator - ------------------------------------------------------------
14:30:54.831 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:54.831 INFO  Funcotator - Picard Version: 3.4.0
14:30:54.831 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:54.831 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:54.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:54.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:54.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:54.831 INFO  Funcotator - Deflater: IntelDeflater
14:30:54.831 INFO  Funcotator - Inflater: IntelInflater
14:30:54.831 INFO  Funcotator - GCS max retries/reopens: 20
14:30:54.831 INFO  Funcotator - Requester pays: disabled
14:30:54.831 INFO  Funcotator - Initializing engine
14:30:54.832 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:30:54.833 INFO  Funcotator - Done initializing engine
14:30:54.833 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:54.833 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:54.833 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder916090786512607971/TranscriptIdFile.txt
14:30:54.833 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:30:54.833 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:54.833 INFO  Funcotator - Initializing data sources...
14:30:54.833 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:54.833 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:54.833 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:54.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:54.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:54.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:54.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:54.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:54.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:54.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:54.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:54.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:54.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:54.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:54.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:54.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:54.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:54.837 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:54.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:54.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:54.857 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:54.857 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:54.904 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:54.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:55.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:55.582 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:30:55.583 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:55.585 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:55.588 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:55.590 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:30:55.590 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:55.591 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:30:55.618 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:55.618 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:30:55	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:30:55.619 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:55.657 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:55.658 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:55.658 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:55.666 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:55.666 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:55.666 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:30:55.667 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:55.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:55.753 INFO  Funcotator - Initializing Funcotator Engine...
14:30:55.753 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:30:55.753 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:30:55.753 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.44280755615542022219.vcf
14:30:55.754 INFO  ProgressMeter - Starting traversal
14:30:55.754 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:30:55.978 INFO  ProgressMeter -             unmapped              0.0                     4           1071.4
14:30:55.978 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:30:55.978 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:30:55.979 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:30:55 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1797259264
14:30:56.071 INFO  Funcotator - ------------------------------------------------------------
14:30:56.071 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:56.071 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:56.071 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:56.071 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:56.071 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:56 PM GMT
14:30:56.071 INFO  Funcotator - ------------------------------------------------------------
14:30:56.071 INFO  Funcotator - ------------------------------------------------------------
14:30:56.071 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:56.071 INFO  Funcotator - Picard Version: 3.4.0
14:30:56.071 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:56.071 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:56.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:56.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:56.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:56.071 INFO  Funcotator - Deflater: IntelDeflater
14:30:56.072 INFO  Funcotator - Inflater: IntelInflater
14:30:56.072 INFO  Funcotator - GCS max retries/reopens: 20
14:30:56.072 INFO  Funcotator - Requester pays: disabled
14:30:56.072 INFO  Funcotator - Initializing engine
14:30:56.073 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:30:56.073 INFO  Funcotator - Done initializing engine
14:30:56.073 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:56.073 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:56.073 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder3112815844345409083/TranscriptIdFile.txt
14:30:56.073 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:30:56.073 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:56.073 INFO  Funcotator - Initializing data sources...
14:30:56.074 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:56.074 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:56.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:56.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:56.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:56.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:56.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:56.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:56.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:56.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:56.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:56.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:56.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:56.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:56.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:56.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:56.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:56.077 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:56.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:56.078 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:56.096 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:56.097 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:56.143 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:56.144 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:56.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:56.863 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:30:56.864 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:56.866 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:56.869 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:56.871 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:30:56.871 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:56.872 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:30:56.900 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:56.900 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:30:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:30:56.900 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:56.940 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:56.941 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:56.941 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:56.949 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:56.950 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:56.950 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:30:56.951 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:56.952 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:57.035 INFO  Funcotator - Initializing Funcotator Engine...
14:30:57.036 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:30:57.036 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:30:57.036 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:30:57.036 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:30:57.036 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:30:57.037 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:30:57.038 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:30:57.038 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:30:57.038 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.311628372863525881911.vcf
14:30:57.038 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:30:57.040 INFO  ProgressMeter - Starting traversal
14:30:57.040 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:30:57.069 INFO  ProgressMeter -             unmapped              0.0                     3           6206.9
14:30:57.069 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:30:57.069 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:30:57.072 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:30:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1937768448
14:30:57.200 INFO  Funcotator - ------------------------------------------------------------
14:30:57.200 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:57.200 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:57.200 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:57.200 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:57.200 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:57 PM GMT
14:30:57.200 INFO  Funcotator - ------------------------------------------------------------
14:30:57.200 INFO  Funcotator - ------------------------------------------------------------
14:30:57.200 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:57.200 INFO  Funcotator - Picard Version: 3.4.0
14:30:57.200 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:57.200 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:57.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:57.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:57.200 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:57.200 INFO  Funcotator - Deflater: IntelDeflater
14:30:57.200 INFO  Funcotator - Inflater: IntelInflater
14:30:57.200 INFO  Funcotator - GCS max retries/reopens: 20
14:30:57.200 INFO  Funcotator - Requester pays: disabled
14:30:57.200 INFO  Funcotator - Initializing engine
14:30:57.201 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:30:57.202 INFO  Funcotator - Done initializing engine
14:30:57.202 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:57.202 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:57.202 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder11282724770992643058/TranscriptIdFile.txt
14:30:57.202 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:30:57.202 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:57.202 INFO  Funcotator - Initializing data sources...
14:30:57.202 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:57.202 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:57.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:57.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:57.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:57.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:57.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:57.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:57.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:57.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:57.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:57.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:57.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:57.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:57.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:57.206 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:57.206 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:57.206 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:57.206 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:57.206 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:57.225 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:57.225 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:57.270 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:57.270 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:58.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:58.060 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:30:58.061 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:58.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:58.066 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:58.068 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:30:58.069 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:58.069 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:30:58.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:58.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:30:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:30:58.104 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:58.142 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:58.142 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:58.143 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:58.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:58.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:58.150 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:30:58.151 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:58.151 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:58.240 INFO  Funcotator - Initializing Funcotator Engine...
14:30:58.240 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:30:58.240 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:30:58.240 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.414507636484194679112.vcf
14:30:58.242 INFO  ProgressMeter - Starting traversal
14:30:58.242 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:30:58.359 INFO  ProgressMeter -             unmapped              0.0                     4           2051.3
14:30:58.359 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:30:58.359 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:30:58.360 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:30:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2267021312
14:30:58.455 INFO  Funcotator - ------------------------------------------------------------
14:30:58.456 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:58.456 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:58.456 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:58.456 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:58.456 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:58 PM GMT
14:30:58.456 INFO  Funcotator - ------------------------------------------------------------
14:30:58.456 INFO  Funcotator - ------------------------------------------------------------
14:30:58.456 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:58.456 INFO  Funcotator - Picard Version: 3.4.0
14:30:58.456 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:58.456 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:58.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:58.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:58.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:58.456 INFO  Funcotator - Deflater: IntelDeflater
14:30:58.456 INFO  Funcotator - Inflater: IntelInflater
14:30:58.456 INFO  Funcotator - GCS max retries/reopens: 20
14:30:58.456 INFO  Funcotator - Requester pays: disabled
14:30:58.456 INFO  Funcotator - Initializing engine
14:30:58.457 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:30:58.457 INFO  Funcotator - Done initializing engine
14:30:58.457 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:58.457 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:58.458 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder3652220639089846178/TranscriptIdFile.txt
14:30:58.458 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:30:58.458 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:58.458 INFO  Funcotator - Initializing data sources...
14:30:58.458 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:58.458 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:58.458 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:58.458 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:58.459 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:58.459 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:58.459 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:58.459 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:58.459 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:58.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:58.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:58.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:58.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:58.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:58.461 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:58.461 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:58.461 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:58.461 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:58.461 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:58.461 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:58.480 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:58.481 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:58.679 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:58.679 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:59.260 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:59.261 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:30:59.262 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:59.264 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:59.266 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:59.269 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:30:59.269 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:59.270 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:30:59.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:59.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:30:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:30:59.299 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:59.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:59.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:59.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:59.345 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:59.346 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:59.346 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:30:59.347 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:59.347 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:59.429 INFO  Funcotator - Initializing Funcotator Engine...
14:30:59.429 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:30:59.429 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:30:59.429 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:30:59.429 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:30:59.430 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:30:59.430 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:30:59.430 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.39967028400516175324.maf
14:30:59.433 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:30:59.434 INFO  ProgressMeter - Starting traversal
14:30:59.434 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:30:59.463 INFO  ProgressMeter -             unmapped              0.0                     3           6206.9
14:30:59.463 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:30:59.463 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:30:59.463 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:30:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2267021312
14:30:59.550 INFO  Funcotator - ------------------------------------------------------------
14:30:59.550 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:30:59.550 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:30:59.550 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:30:59.550 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:30:59.550 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:30:59 PM GMT
14:30:59.550 INFO  Funcotator - ------------------------------------------------------------
14:30:59.550 INFO  Funcotator - ------------------------------------------------------------
14:30:59.550 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:30:59.550 INFO  Funcotator - Picard Version: 3.4.0
14:30:59.550 INFO  Funcotator - Built for Spark Version: 3.5.0
14:30:59.550 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:30:59.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:30:59.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:30:59.550 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:30:59.550 INFO  Funcotator - Deflater: IntelDeflater
14:30:59.550 INFO  Funcotator - Inflater: IntelInflater
14:30:59.550 INFO  Funcotator - GCS max retries/reopens: 20
14:30:59.550 INFO  Funcotator - Requester pays: disabled
14:30:59.550 INFO  Funcotator - Initializing engine
14:30:59.551 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:30:59.552 INFO  Funcotator - Done initializing engine
14:30:59.552 INFO  Funcotator - Skipping sequence dictionary validation.
14:30:59.552 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:30:59.552 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6474920849975799027/TranscriptIdFile.txt
14:30:59.552 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:30:59.552 INFO  FuncotatorEngine - Transcript parsing complete.
14:30:59.552 INFO  Funcotator - Initializing data sources...
14:30:59.552 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:30:59.552 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:30:59.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:59.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:59.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:59.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:59.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:30:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:30:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:30:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:30:59.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:30:59.555 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:30:59.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:30:59.556 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:30:59.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:30:59.577 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:30:59.629 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:30:59.629 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:00.294 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:00.294 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:00.295 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:00.297 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:00.300 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:00.303 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:00.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:00.304 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:00.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:00.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:00.339 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:00.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:00.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:00.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:00.386 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:00.387 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:00.387 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:00.388 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:00.388 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:00.471 INFO  Funcotator - Initializing Funcotator Engine...
14:31:00.471 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:00.471 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:00.471 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.418399301515709233923.maf
14:31:00.471 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:00.473 INFO  ProgressMeter - Starting traversal
14:31:00.473 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:00.650 INFO  ProgressMeter -             unmapped              0.0                     4           1355.9
14:31:00.650 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:00.650 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:00.650 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2778726400
14:31:00.817 INFO  Funcotator - ------------------------------------------------------------
14:31:00.817 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:00.817 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:00.817 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:00.817 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:00.817 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:00 PM GMT
14:31:00.817 INFO  Funcotator - ------------------------------------------------------------
14:31:00.817 INFO  Funcotator - ------------------------------------------------------------
14:31:00.817 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:00.817 INFO  Funcotator - Picard Version: 3.4.0
14:31:00.817 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:00.817 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:00.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:00.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:00.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:00.817 INFO  Funcotator - Deflater: IntelDeflater
14:31:00.817 INFO  Funcotator - Inflater: IntelInflater
14:31:00.817 INFO  Funcotator - GCS max retries/reopens: 20
14:31:00.817 INFO  Funcotator - Requester pays: disabled
14:31:00.817 INFO  Funcotator - Initializing engine
14:31:00.819 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:31:00.820 INFO  Funcotator - Done initializing engine
14:31:00.820 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:00.820 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:00.821 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4175171759526509221/TranscriptIdFile.txt
14:31:00.821 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:31:00.821 INFO  FuncotatorEngine - Transcript parsing complete.
14:31:00.821 INFO  Funcotator - Initializing data sources...
14:31:00.821 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:00.821 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:00.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:00.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:00.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:00.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:00.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:00.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:00.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:00.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:00.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:00.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:00.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:00.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:00.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:00.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:00.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:00.824 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:00.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:00.825 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:00.868 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:00.868 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:00.951 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:00.952 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:01.624 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:01.624 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:01.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:01.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:01.630 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:01.632 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:01.633 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:01.633 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:01.661 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:01.661 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:01.661 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:01.700 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:01.700 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:01.701 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:01.708 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:01.709 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:01.709 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:01.710 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:01.710 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:01.794 INFO  Funcotator - Initializing Funcotator Engine...
14:31:01.794 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:01.794 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:31:01.794 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:31:01.795 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:31:01.795 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:31:01.795 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:01.795 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.38047005873011521848.maf
14:31:01.796 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:01.798 INFO  ProgressMeter - Starting traversal
14:31:01.798 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:01.836 INFO  ProgressMeter -             unmapped              0.0                     3           4736.8
14:31:01.836 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:31:01.836 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:01.836 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2778726400
14:31:01.956 INFO  Funcotator - ------------------------------------------------------------
14:31:01.956 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:01.956 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:01.956 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:01.956 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:01.956 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:01 PM GMT
14:31:01.956 INFO  Funcotator - ------------------------------------------------------------
14:31:01.956 INFO  Funcotator - ------------------------------------------------------------
14:31:01.956 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:01.956 INFO  Funcotator - Picard Version: 3.4.0
14:31:01.956 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:01.956 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:01.956 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:01.956 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:01.956 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:01.956 INFO  Funcotator - Deflater: IntelDeflater
14:31:01.956 INFO  Funcotator - Inflater: IntelInflater
14:31:01.956 INFO  Funcotator - GCS max retries/reopens: 20
14:31:01.956 INFO  Funcotator - Requester pays: disabled
14:31:01.956 INFO  Funcotator - Initializing engine
14:31:01.957 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:31:01.958 INFO  Funcotator - Done initializing engine
14:31:01.958 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:01.958 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:01.958 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder1420072546774943277/TranscriptIdFile.txt
14:31:01.958 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:31:01.958 INFO  FuncotatorEngine - Transcript parsing complete.
14:31:01.958 INFO  Funcotator - Initializing data sources...
14:31:01.958 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:01.958 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:01.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:01.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:01.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:01.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:01.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:01.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:01.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:01.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:01.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:01.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:01.961 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:01.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:01.962 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:01.981 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:01.981 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:02.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:02.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:02.611 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:02.611 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:02.612 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:02.614 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:02.617 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:02.619 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:02.620 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:02.620 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:02.647 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:02.648 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:02.648 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:02.687 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:02.688 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:02.688 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:02.696 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:02.696 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:02.696 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:02.697 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:02.698 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:02.786 INFO  Funcotator - Initializing Funcotator Engine...
14:31:02.786 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:02.786 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:02.786 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.413712692768099103867.maf
14:31:02.786 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:02.787 INFO  ProgressMeter - Starting traversal
14:31:02.788 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:02.904 INFO  ProgressMeter -             unmapped              0.0                     4           2069.0
14:31:02.904 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:02.904 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:02.904 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:02 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2778726400
14:31:03.010 INFO  Funcotator - ------------------------------------------------------------
14:31:03.010 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:03.010 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:03.010 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:03.010 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:03.010 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:03 PM GMT
14:31:03.010 INFO  Funcotator - ------------------------------------------------------------
14:31:03.010 INFO  Funcotator - ------------------------------------------------------------
14:31:03.010 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:03.010 INFO  Funcotator - Picard Version: 3.4.0
14:31:03.010 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:03.010 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:03.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:03.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:03.010 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:03.010 INFO  Funcotator - Deflater: IntelDeflater
14:31:03.010 INFO  Funcotator - Inflater: IntelInflater
14:31:03.010 INFO  Funcotator - GCS max retries/reopens: 20
14:31:03.010 INFO  Funcotator - Requester pays: disabled
14:31:03.010 INFO  Funcotator - Initializing engine
14:31:03.013 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:31:03.014 INFO  Funcotator - Done initializing engine
14:31:03.014 INFO  Funcotator - Validating sequence dictionaries...
14:31:03.015 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:03.015 INFO  Funcotator - Initializing data sources...
14:31:03.015 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:03.015 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:03.015 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:03.015 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:03.015 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:03.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:03.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:03.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:03.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:03.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:03.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:03.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:03.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:03.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:03.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:03.018 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:03.018 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:03.018 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:03.018 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:03.018 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:03.038 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:03.038 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:03.085 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:03.085 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:03.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:03.677 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:03.678 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:03.681 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:03.685 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:03.688 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:03.689 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:03.690 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:03.718 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:03.718 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:03.719 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:03.759 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:03.759 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:03.760 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:03.767 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:03.768 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:03.768 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:03.769 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:03.769 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:03.852 INFO  Funcotator - Initializing Funcotator Engine...
14:31:03.853 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:03.853 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:03.853 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator799900121776745729.vcf
14:31:03.854 INFO  ProgressMeter - Starting traversal
14:31:03.854 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:06.192 INFO  ProgressMeter -             unmapped              0.0                   198           5081.3
14:31:06.192 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:06.192 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:06.202 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:06 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2814377984
14:31:06.203 WARN  gatk -   VCF Elapsed Time: 3.296164148s
14:31:06.204 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator799900121776745729.vcf
14:31:06.206 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:31:06.311 INFO  Funcotator - ------------------------------------------------------------
14:31:06.311 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:06.311 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:06.311 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:06.311 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:06.311 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:06 PM GMT
14:31:06.311 INFO  Funcotator - ------------------------------------------------------------
14:31:06.311 INFO  Funcotator - ------------------------------------------------------------
14:31:06.311 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:06.311 INFO  Funcotator - Picard Version: 3.4.0
14:31:06.311 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:06.311 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:06.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:06.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:06.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:06.311 INFO  Funcotator - Deflater: IntelDeflater
14:31:06.311 INFO  Funcotator - Inflater: IntelInflater
14:31:06.311 INFO  Funcotator - GCS max retries/reopens: 20
14:31:06.311 INFO  Funcotator - Requester pays: disabled
14:31:06.311 INFO  Funcotator - Initializing engine
14:31:06.314 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:31:06.315 INFO  Funcotator - Done initializing engine
14:31:06.315 INFO  Funcotator - Validating sequence dictionaries...
14:31:06.315 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:06.315 INFO  Funcotator - Initializing data sources...
14:31:06.315 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:06.315 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:06.315 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:06.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:06.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:06.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:06.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:06.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:06.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:06.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:06.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:06.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:06.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:06.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:06.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:06.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:06.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:06.318 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:06.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:06.319 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:06.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:06.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:06.383 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:06.384 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:06.970 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:06.970 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:06.971 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:06.973 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:06.976 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:06.978 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:06.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:06.979 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:07.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:07.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:07.007 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:07.046 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:07.046 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:07.046 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:07.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:07.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:07.054 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:07.055 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:07.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:07.197 INFO  Funcotator - Initializing Funcotator Engine...
14:31:07.198 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:07.198 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:07.198 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator10743813409221755101.maf
14:31:07.198 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:07.199 INFO  ProgressMeter - Starting traversal
14:31:07.199 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:09.203 INFO  ProgressMeter -             unmapped              0.0                   198           5928.1
14:31:09.203 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:09.203 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:09.203 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2814377984
14:31:09.204 WARN  gatk -   MAF Elapsed Time: 2.992923842s
14:31:09.296 INFO  Funcotator - ------------------------------------------------------------
14:31:09.296 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:09.296 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:09.296 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:09.296 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:09.296 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:09 PM GMT
14:31:09.296 INFO  Funcotator - ------------------------------------------------------------
14:31:09.296 INFO  Funcotator - ------------------------------------------------------------
14:31:09.296 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:09.296 INFO  Funcotator - Picard Version: 3.4.0
14:31:09.296 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:09.296 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:09.296 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:09.296 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:09.296 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:09.296 INFO  Funcotator - Deflater: IntelDeflater
14:31:09.296 INFO  Funcotator - Inflater: IntelInflater
14:31:09.296 INFO  Funcotator - GCS max retries/reopens: 20
14:31:09.296 INFO  Funcotator - Requester pays: disabled
14:31:09.296 INFO  Funcotator - Initializing engine
14:31:09.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
14:31:09.300 INFO  Funcotator - Done initializing engine
14:31:09.300 INFO  Funcotator - Validating sequence dictionaries...
14:31:09.300 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:09.300 INFO  Funcotator - Initializing data sources...
14:31:09.300 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:09.300 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:09.301 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:09.301 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:09.301 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:09.301 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:09.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:09.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:09.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:09.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:09.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:09.303 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:09.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:09.304 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:09.324 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:09.324 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:09.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:09.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:09.984 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:09.984 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:09.986 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:09.989 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:09.991 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:09.993 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:09.994 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:09.994 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:10.022 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:10.023 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:10.023 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:10.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:10.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:10.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:10.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:10.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:10.071 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:10.072 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:10.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:10.157 INFO  Funcotator - Initializing Funcotator Engine...
14:31:10.157 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:10.157 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:10.157 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator5830788641468001448.vcf
14:31:10.160 INFO  ProgressMeter - Starting traversal
14:31:10.160 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:11.223 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:31:11.224 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:31:12.054 INFO  ProgressMeter -             unmapped              0.0                   168           5322.1
14:31:12.054 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:31:12.054 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:31:12.060 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:12 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2868903936
14:31:12.061 WARN  gatk -   VCF Elapsed Time: 2.852330624s
14:31:12.061 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator5830788641468001448.vcf
14:31:12.064 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
14:31:12.165 INFO  Funcotator - ------------------------------------------------------------
14:31:12.165 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:12.165 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:12.165 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:12.165 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:12.165 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:12 PM GMT
14:31:12.165 INFO  Funcotator - ------------------------------------------------------------
14:31:12.165 INFO  Funcotator - ------------------------------------------------------------
14:31:12.165 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:12.165 INFO  Funcotator - Picard Version: 3.4.0
14:31:12.165 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:12.165 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:12.165 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:12.165 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:12.165 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:12.165 INFO  Funcotator - Deflater: IntelDeflater
14:31:12.165 INFO  Funcotator - Inflater: IntelInflater
14:31:12.165 INFO  Funcotator - GCS max retries/reopens: 20
14:31:12.165 INFO  Funcotator - Requester pays: disabled
14:31:12.165 INFO  Funcotator - Initializing engine
14:31:12.168 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
14:31:12.169 INFO  Funcotator - Done initializing engine
14:31:12.169 INFO  Funcotator - Validating sequence dictionaries...
14:31:12.169 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:12.169 INFO  Funcotator - Initializing data sources...
14:31:12.169 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:12.169 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:12.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:12.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:12.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:12.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:12.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:12.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:12.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:12.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:12.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:12.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:12.172 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:12.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:12.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:12.199 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:12.199 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:12.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:12.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:12.865 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:12.865 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:12.866 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:12.869 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:12.872 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:12.874 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:12.874 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:12.875 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:12.904 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:12.904 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:12.904 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:12.948 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:12.948 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:12.949 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:12.971 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:12.972 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:12.972 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:12.973 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:12.973 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:13.073 INFO  Funcotator - Initializing Funcotator Engine...
14:31:13.074 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:13.074 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:13.074 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator12874486396303521277.maf
14:31:13.074 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:13.075 INFO  ProgressMeter - Starting traversal
14:31:13.076 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:14.246 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:31:14.246 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:31:14.996 INFO  ProgressMeter -             unmapped              0.0                   168           5250.0
14:31:14.996 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:31:14.996 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:31:14.996 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:14 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3084910592
14:31:14.996 WARN  gatk -   MAF Elapsed Time: 2.927702591s
14:31:15.089 INFO  Funcotator - ------------------------------------------------------------
14:31:15.089 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:15.089 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:15.089 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:15.089 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:15.089 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:15 PM GMT
14:31:15.089 INFO  Funcotator - ------------------------------------------------------------
14:31:15.089 INFO  Funcotator - ------------------------------------------------------------
14:31:15.089 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:15.089 INFO  Funcotator - Picard Version: 3.4.0
14:31:15.089 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:15.089 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:15.089 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:15.089 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:15.089 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:15.089 INFO  Funcotator - Deflater: IntelDeflater
14:31:15.089 INFO  Funcotator - Inflater: IntelInflater
14:31:15.089 INFO  Funcotator - GCS max retries/reopens: 20
14:31:15.089 INFO  Funcotator - Requester pays: disabled
14:31:15.089 INFO  Funcotator - Initializing engine
14:31:15.092 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
14:31:15.093 INFO  Funcotator - Done initializing engine
14:31:15.093 INFO  Funcotator - Validating sequence dictionaries...
14:31:15.093 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:15.093 INFO  Funcotator - Initializing data sources...
14:31:15.093 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:15.093 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:15.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:15.095 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:15.095 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:15.095 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:15.095 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:15.095 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:15.096 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:15.105 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:15.105 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:15.105 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:15.105 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:15.106 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:15.106 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:15.125 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:15.125 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:15.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:15.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:15.724 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:15.724 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:15.725 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:15.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:15.730 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:15.732 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:15.733 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:15.733 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:15.760 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:15.760 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:15.760 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:15.799 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:15.800 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:15.800 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:15.808 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:15.808 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:15.808 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:15.809 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:15.809 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:15.894 INFO  Funcotator - Initializing Funcotator Engine...
14:31:15.894 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:15.894 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:15.894 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator13782525320402163369.vcf
14:31:15.896 INFO  ProgressMeter - Starting traversal
14:31:15.896 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:15.906 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
14:31:15.906 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:15.906 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:15.907 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:15 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3084910592
14:31:15.907 WARN  gatk -   VCF Elapsed Time: 0.908643365s
14:31:15.908 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator13782525320402163369.vcf
14:31:15.910 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
14:31:15.999 INFO  Funcotator - ------------------------------------------------------------
14:31:15.999 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:15.999 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:15.999 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:15.999 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:15.999 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:15 PM GMT
14:31:15.999 INFO  Funcotator - ------------------------------------------------------------
14:31:15.999 INFO  Funcotator - ------------------------------------------------------------
14:31:16.000 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:16.000 INFO  Funcotator - Picard Version: 3.4.0
14:31:16.000 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:16.000 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:16.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:16.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:16.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:16.000 INFO  Funcotator - Deflater: IntelDeflater
14:31:16.000 INFO  Funcotator - Inflater: IntelInflater
14:31:16.000 INFO  Funcotator - GCS max retries/reopens: 20
14:31:16.000 INFO  Funcotator - Requester pays: disabled
14:31:16.000 INFO  Funcotator - Initializing engine
14:31:16.002 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
14:31:16.003 INFO  Funcotator - Done initializing engine
14:31:16.003 INFO  Funcotator - Validating sequence dictionaries...
14:31:16.003 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:16.003 INFO  Funcotator - Initializing data sources...
14:31:16.003 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:16.003 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:16.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:16.005 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:16.005 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:16.005 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:16.005 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:16.005 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:16.006 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:16.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:16.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:16.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:16.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:16.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:16.630 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:16.630 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:16.631 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:16.633 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:16.636 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:16.639 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:16.639 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:16.639 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:16.667 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:16.667 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:16	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:16.667 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:16.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:16.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:16.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:16.714 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:16.714 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:16.714 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:16.715 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:16.716 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:16.801 INFO  Funcotator - Initializing Funcotator Engine...
14:31:16.801 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:16.801 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.
14:31:16.801 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator17059286225766026862.maf
14:31:16.801 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:16.802 INFO  ProgressMeter - Starting traversal
14:31:16.802 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:16.814 INFO  ProgressMeter -             unmapped              0.0                     1           5000.0
14:31:16.814 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:16.814 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:16.814 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:16 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3084910592
14:31:16.814 WARN  gatk -   MAF Elapsed Time: 0.903875291s
14:31:16.911 INFO  Funcotator - ------------------------------------------------------------
14:31:16.911 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:16.911 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:16.911 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:16.911 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:16.911 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:16 PM GMT
14:31:16.911 INFO  Funcotator - ------------------------------------------------------------
14:31:16.911 INFO  Funcotator - ------------------------------------------------------------
14:31:16.911 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:16.911 INFO  Funcotator - Picard Version: 3.4.0
14:31:16.911 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:16.911 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:16.911 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:16.911 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:16.911 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:16.911 INFO  Funcotator - Deflater: IntelDeflater
14:31:16.911 INFO  Funcotator - Inflater: IntelInflater
14:31:16.911 INFO  Funcotator - GCS max retries/reopens: 20
14:31:16.911 INFO  Funcotator - Requester pays: disabled
14:31:16.911 INFO  Funcotator - Initializing engine
14:31:16.947 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
14:31:16.971 INFO  Funcotator - Done initializing engine
14:31:16.971 INFO  Funcotator - Validating sequence dictionaries...
14:31:16.979 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:16.979 INFO  Funcotator - Initializing data sources...
14:31:16.979 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:16.979 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:16.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:16.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:16.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:16.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:16.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:16.981 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:16.981 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:16.982 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:16.982 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:16.982 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:16.982 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:16.983 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:16.983 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:16.983 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:16.983 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:16.983 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:17.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:17.014 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:17.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:17.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:17.620 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:17.620 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:17.621 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:17.622 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:17.624 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:17.626 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:17.693 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:17.693 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:17.694 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:17.703 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:17.703 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:17.704 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:17.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:17.706 INFO  Funcotator - Initializing Funcotator Engine...
14:31:17.710 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:17.710 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator16075608941875083205.vcf
14:31:17.728 INFO  ProgressMeter - Starting traversal
14:31:17.728 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:17.756 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000374877.7 for variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C): Reference allele runs off end of coding sequence.  Cannot yet handle this case.
14:31:17.758 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:31:17.762 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:17.765 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:17.765 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:17.765 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:17.765 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:17.765 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:17.766 INFO  ProgressMeter -             unmapped              0.0                     5           7894.7
14:31:17.766 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:31:17.766 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:17.774 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3084910592
14:31:17.775 WARN  gatk -   VCF Elapsed Time: 0.959526599s
14:31:17.775 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator16075608941875083205.vcf
14:31:17.785 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
14:31:17.883 INFO  Funcotator - ------------------------------------------------------------
14:31:17.883 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:17.883 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:17.883 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:17.883 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:17.883 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:17 PM GMT
14:31:17.883 INFO  Funcotator - ------------------------------------------------------------
14:31:17.883 INFO  Funcotator - ------------------------------------------------------------
14:31:17.883 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:17.883 INFO  Funcotator - Picard Version: 3.4.0
14:31:17.883 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:17.883 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:17.883 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:17.883 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:17.883 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:17.883 INFO  Funcotator - Deflater: IntelDeflater
14:31:17.883 INFO  Funcotator - Inflater: IntelInflater
14:31:17.883 INFO  Funcotator - GCS max retries/reopens: 20
14:31:17.884 INFO  Funcotator - Requester pays: disabled
14:31:17.884 INFO  Funcotator - Initializing engine
14:31:17.914 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
14:31:17.936 INFO  Funcotator - Done initializing engine
14:31:17.936 INFO  Funcotator - Validating sequence dictionaries...
14:31:17.943 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:17.943 INFO  Funcotator - Initializing data sources...
14:31:17.943 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:17.943 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:17.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:17.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:17.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:17.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:17.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:17.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:17.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:17.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:17.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:17.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:17.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:17.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:17.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:17.946 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:17.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:17.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:17.964 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:17.965 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:18.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:18.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:18.599 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:18.599 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:18.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:18.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:18.604 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:18.605 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:18.671 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:18.671 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:18.671 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:18.679 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:18.679 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:18.680 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:18.680 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:18.681 INFO  Funcotator - Initializing Funcotator Engine...
14:31:18.685 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:18.685 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator9468952383671723236.maf
14:31:18.687 INFO  ProgressMeter - Starting traversal
14:31:18.687 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:18.712 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000374877.7 for variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C): Reference allele runs off end of coding sequence.  Cannot yet handle this case.
14:31:18.712 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:31:18.714 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:18.717 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:18.717 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:31:18.717 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:18.717 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:18.718 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:31:18.719 INFO  ProgressMeter -             unmapped              0.0                     5           9375.0
14:31:18.719 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:31:18.719 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:18.719 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3084910592
14:31:18.719 WARN  gatk -   MAF Elapsed Time: 0.926784987s
14:31:18.810 INFO  Funcotator - ------------------------------------------------------------
14:31:18.810 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:18.810 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:18.810 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:18.810 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:18.810 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:18 PM GMT
14:31:18.810 INFO  Funcotator - ------------------------------------------------------------
14:31:18.810 INFO  Funcotator - ------------------------------------------------------------
14:31:18.810 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:18.810 INFO  Funcotator - Picard Version: 3.4.0
14:31:18.810 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:18.810 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:18.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:18.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:18.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:18.810 INFO  Funcotator - Deflater: IntelDeflater
14:31:18.810 INFO  Funcotator - Inflater: IntelInflater
14:31:18.810 INFO  Funcotator - GCS max retries/reopens: 20
14:31:18.810 INFO  Funcotator - Requester pays: disabled
14:31:18.810 INFO  Funcotator - Initializing engine
14:31:18.813 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
14:31:18.817 INFO  Funcotator - Done initializing engine
14:31:18.817 INFO  Funcotator - Validating sequence dictionaries...
14:31:18.817 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:18.817 INFO  Funcotator - Initializing data sources...
14:31:18.817 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:18.817 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:18.818 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:18.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:18.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:18.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:18.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:18.820 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:18.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:18.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:18.839 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:18.839 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:18.884 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:18.885 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:19.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:19.467 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:19.468 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:19.470 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:19.473 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:19.475 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:19.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:19.476 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:19.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:19.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:19	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:19.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:19.543 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:19.543 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:19.544 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:19.551 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:19.552 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:19.552 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:19.553 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:19.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:19.641 INFO  Funcotator - Initializing Funcotator Engine...
14:31:19.641 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:19.641 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:19.641 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator4793281031739628603.vcf
14:31:19.645 INFO  ProgressMeter - Starting traversal
14:31:19.645 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:25.221 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:31:25.222 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:31:25.223 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16210.1
14:31:25.223 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:31:25.223 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:31:25.246 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3084910592
14:31:25.246 WARN  gatk -   VCF Elapsed Time: 6.52426503s
14:31:25.247 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator4793281031739628603.vcf
14:31:25.256 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
14:31:25.365 INFO  Funcotator - ------------------------------------------------------------
14:31:25.365 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:25.365 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:25.365 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:25.365 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:25.365 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:25 PM GMT
14:31:25.365 INFO  Funcotator - ------------------------------------------------------------
14:31:25.365 INFO  Funcotator - ------------------------------------------------------------
14:31:25.365 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:25.365 INFO  Funcotator - Picard Version: 3.4.0
14:31:25.365 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:25.365 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:25.365 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:25.365 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:25.365 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:25.365 INFO  Funcotator - Deflater: IntelDeflater
14:31:25.365 INFO  Funcotator - Inflater: IntelInflater
14:31:25.365 INFO  Funcotator - GCS max retries/reopens: 20
14:31:25.365 INFO  Funcotator - Requester pays: disabled
14:31:25.365 INFO  Funcotator - Initializing engine
14:31:25.367 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
14:31:25.369 INFO  Funcotator - Done initializing engine
14:31:25.369 INFO  Funcotator - Validating sequence dictionaries...
14:31:25.369 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:25.369 INFO  Funcotator - Initializing data sources...
14:31:25.369 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:25.369 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:25.369 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:25.370 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:25.370 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:25.370 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:25.370 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:25.370 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:25.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:25.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:25.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:25.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:25.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:25.372 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:25.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:25.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:25.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:25.437 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:25.437 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:26.037 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:26.037 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:26.038 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:26.040 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:26.043 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:26.045 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:26.045 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:26.046 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:26.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:26.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:26	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:26.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:26.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:26.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:26.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:26.121 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:26.121 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:26.121 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:26.122 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:26.123 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:26.206 INFO  Funcotator - Initializing Funcotator Engine...
14:31:26.207 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:26.207 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:26.207 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator86387074462773228.maf
14:31:26.207 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:26.208 INFO  ProgressMeter - Starting traversal
14:31:26.208 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:31.416 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:31:31.416 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:31:31.417 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17358.4
14:31:31.417 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:31:31.417 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:31:31.417 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:31 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3084910592
14:31:31.418 WARN  gatk -   MAF Elapsed Time: 6.141932508s
14:31:31.529 INFO  Funcotator - ------------------------------------------------------------
14:31:31.529 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:31.529 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:31.529 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:31.529 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:31.529 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:31 PM GMT
14:31:31.529 INFO  Funcotator - ------------------------------------------------------------
14:31:31.529 INFO  Funcotator - ------------------------------------------------------------
14:31:31.529 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:31.529 INFO  Funcotator - Picard Version: 3.4.0
14:31:31.529 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:31.529 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:31.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:31.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:31.529 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:31.529 INFO  Funcotator - Deflater: IntelDeflater
14:31:31.529 INFO  Funcotator - Inflater: IntelInflater
14:31:31.529 INFO  Funcotator - GCS max retries/reopens: 20
14:31:31.529 INFO  Funcotator - Requester pays: disabled
14:31:31.529 INFO  Funcotator - Initializing engine
14:31:31.532 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:31:31.533 INFO  Funcotator - Done initializing engine
14:31:31.533 INFO  Funcotator - Validating sequence dictionaries...
14:31:31.533 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:31.533 INFO  Funcotator - Initializing data sources...
14:31:31.533 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:31.533 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:31.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:31.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:31.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:31.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:31.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:31.535 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:31.535 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:31.535 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:31.535 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:31.535 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:31.536 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:31.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:31.537 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:31.556 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:31.556 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:31.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:31.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:32.186 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:32.186 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:32.187 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:32.189 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:32.192 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:32.194 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:32.194 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:32.194 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:32.222 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:32.222 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:32	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:32.222 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:32.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:32.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:32.263 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:32.270 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:32.271 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:32.271 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:32.272 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:32.272 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:32.360 INFO  Funcotator - Initializing Funcotator Engine...
14:31:32.360 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:32.360 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:32.360 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator7625200365687360411.vcf
14:31:32.362 INFO  ProgressMeter - Starting traversal
14:31:32.362 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:34.380 INFO  ProgressMeter -             unmapped              0.0                   198           5887.0
14:31:34.380 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:34.380 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:34.389 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:34 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3084910592
14:31:34.485 INFO  Funcotator - ------------------------------------------------------------
14:31:34.485 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:34.485 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:34.485 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:34.485 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:34.485 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:34 PM GMT
14:31:34.485 INFO  Funcotator - ------------------------------------------------------------
14:31:34.485 INFO  Funcotator - ------------------------------------------------------------
14:31:34.485 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:34.485 INFO  Funcotator - Picard Version: 3.4.0
14:31:34.485 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:34.485 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:34.485 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:34.485 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:34.485 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:34.485 INFO  Funcotator - Deflater: IntelDeflater
14:31:34.485 INFO  Funcotator - Inflater: IntelInflater
14:31:34.485 INFO  Funcotator - GCS max retries/reopens: 20
14:31:34.485 INFO  Funcotator - Requester pays: disabled
14:31:34.485 INFO  Funcotator - Initializing engine
14:31:34.488 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:31:34.489 INFO  Funcotator - Done initializing engine
14:31:34.489 INFO  Funcotator - Validating sequence dictionaries...
14:31:34.489 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:34.489 INFO  Funcotator - Initializing data sources...
14:31:34.489 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:34.489 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:34.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:34.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:34.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:34.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:34.490 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:34.491 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:34.492 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:34.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:34.512 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:34.512 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:34.558 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:34.559 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:35.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:35.147 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:35.148 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:35.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:35.153 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:35.155 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:35.156 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:35.156 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:35.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:35.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:35.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:35.223 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:35.224 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:35.224 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:35.232 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:35.232 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:35.232 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:35.233 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:35.233 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:35.320 INFO  Funcotator - Initializing Funcotator Engine...
14:31:35.321 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:35.321 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:35.321 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator8197841440170153954.maf
14:31:35.321 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:35.322 INFO  ProgressMeter - Starting traversal
14:31:35.322 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:37.316 INFO  ProgressMeter -             unmapped              0.0                   198           5957.9
14:31:37.316 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:37.316 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:37.317 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3084910592
14:31:37.413 INFO  Funcotator - ------------------------------------------------------------
14:31:37.413 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:37.413 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:37.413 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:37.414 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:37.414 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:37 PM GMT
14:31:37.414 INFO  Funcotator - ------------------------------------------------------------
14:31:37.414 INFO  Funcotator - ------------------------------------------------------------
14:31:37.414 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:37.414 INFO  Funcotator - Picard Version: 3.4.0
14:31:37.414 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:37.414 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:37.414 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:37.414 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:37.414 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:37.414 INFO  Funcotator - Deflater: IntelDeflater
14:31:37.414 INFO  Funcotator - Inflater: IntelInflater
14:31:37.414 INFO  Funcotator - GCS max retries/reopens: 20
14:31:37.414 INFO  Funcotator - Requester pays: disabled
14:31:37.414 INFO  Funcotator - Initializing engine
14:31:37.416 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:31:37.417 INFO  Funcotator - Done initializing engine
14:31:37.417 INFO  Funcotator - Validating sequence dictionaries...
14:31:37.418 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:37.418 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3084910592
14:31:37.510 INFO  Funcotator - ------------------------------------------------------------
14:31:37.510 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:37.510 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:37.510 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:37.510 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:37.510 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:37 PM GMT
14:31:37.510 INFO  Funcotator - ------------------------------------------------------------
14:31:37.510 INFO  Funcotator - ------------------------------------------------------------
14:31:37.510 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:37.510 INFO  Funcotator - Picard Version: 3.4.0
14:31:37.510 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:37.510 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:37.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:37.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:37.510 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:37.510 INFO  Funcotator - Deflater: IntelDeflater
14:31:37.510 INFO  Funcotator - Inflater: IntelInflater
14:31:37.510 INFO  Funcotator - GCS max retries/reopens: 20
14:31:37.510 INFO  Funcotator - Requester pays: disabled
14:31:37.510 INFO  Funcotator - Initializing engine
14:31:37.511 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:31:37.538 INFO  Funcotator - Done initializing engine
14:31:37.538 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:37.538 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:37.538 INFO  Funcotator - Initializing data sources...
14:31:37.538 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:37.538 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:37.538 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.538 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:37.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.539 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:37.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.539 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:37.540 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.540 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:37.541 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.541 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:37.542 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.552 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.561 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.570 INFO  Funcotator - Initializing Funcotator Engine...
14:31:37.577 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:37.577 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9034234125402877944.vcf
14:31:37.590 INFO  ProgressMeter - Starting traversal
14:31:37.590 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:37.618 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
14:31:37.618 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:31:37.618 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:37.624 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3084910592
14:31:37.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9034234125402877944.vcf
14:31:37.732 INFO  Funcotator - ------------------------------------------------------------
14:31:37.732 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:37.732 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:37.732 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:37.732 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:37.732 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:37 PM GMT
14:31:37.732 INFO  Funcotator - ------------------------------------------------------------
14:31:37.732 INFO  Funcotator - ------------------------------------------------------------
14:31:37.732 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:37.732 INFO  Funcotator - Picard Version: 3.4.0
14:31:37.732 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:37.732 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:37.732 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:37.732 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:37.732 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:37.732 INFO  Funcotator - Deflater: IntelDeflater
14:31:37.732 INFO  Funcotator - Inflater: IntelInflater
14:31:37.732 INFO  Funcotator - GCS max retries/reopens: 20
14:31:37.732 INFO  Funcotator - Requester pays: disabled
14:31:37.732 INFO  Funcotator - Initializing engine
14:31:37.734 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:31:37.736 INFO  Funcotator - Done initializing engine
14:31:37.736 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:37.736 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:37.736 INFO  Funcotator - Initializing data sources...
14:31:37.736 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:37.736 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:37.736 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:37.736 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:37.736 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:37.736 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:37.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:37.737 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:37.737 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:37.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:37.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:37.738 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:37.738 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:37.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:37.740 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:37.741 INFO  Funcotator - Initializing Funcotator Engine...
14:31:37.741 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:37.741 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.
14:31:37.742 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8202257143855776188.vcf
14:31:37.745 INFO  ProgressMeter - Starting traversal
14:31:37.745 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:37.754 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
14:31:37.754 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:31:37.754 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:31:37.757 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3084910592
14:31:37.758 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8202257143855776188.vcf
14:31:37.860 INFO  Funcotator - ------------------------------------------------------------
14:31:37.860 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:37.860 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:37.860 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:37.860 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:37.860 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:37 PM GMT
14:31:37.860 INFO  Funcotator - ------------------------------------------------------------
14:31:37.860 INFO  Funcotator - ------------------------------------------------------------
14:31:37.860 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:37.860 INFO  Funcotator - Picard Version: 3.4.0
14:31:37.860 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:37.860 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:37.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:37.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:37.860 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:37.860 INFO  Funcotator - Deflater: IntelDeflater
14:31:37.860 INFO  Funcotator - Inflater: IntelInflater
14:31:37.860 INFO  Funcotator - GCS max retries/reopens: 20
14:31:37.860 INFO  Funcotator - Requester pays: disabled
14:31:37.860 INFO  Funcotator - Initializing engine
14:31:37.861 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
14:31:37.875 INFO  Funcotator - Done initializing engine
14:31:37.875 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:37.875 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:37.875 INFO  Funcotator - Initializing data sources...
14:31:37.875 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:37.875 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:37.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:37.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.876 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:37.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.876 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:37.877 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:37.877 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:37.878 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.878 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:37.878 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.886 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.895 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:37.904 INFO  Funcotator - Initializing Funcotator Engine...
14:31:37.910 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:37.910 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11540015486230834038.vcf
14:31:37.921 INFO  ProgressMeter - Starting traversal
14:31:37.921 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:37.925 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
14:31:37.926 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
14:31:37.926 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.926 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:37.926 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:31:37.926 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:31:37.929 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.929 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:37.929 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:31:37.929 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:31:37.929 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
14:31:37.930 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
14:31:37.930 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.930 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:37.930 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:31:37.930 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:31:37.931 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
14:31:37.931 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
14:31:37.931 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:31:37.931 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:31:37.931 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:31:37.931 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:31:37.932 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.932 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:37.933 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:31:37.933 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:31:37.933 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.933 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:37.934 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:31:37.934 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:31:37.934 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
14:31:37.935 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
14:31:37.935 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:31:37.935 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:37.935 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:31:37.935 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:31:37.935 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
14:31:37.936 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
14:31:37.936 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.936 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:37.936 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:31:37.936 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:31:37.937 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:31:37.937 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:37.937 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:31:37.937 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:31:37.938 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
14:31:37.938 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
14:31:37.938 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:37.938 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:37.939 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:31:37.939 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:31:37.939 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
14:31:37.939 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:31:37.939 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:37.944 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3084910592
14:31:37.945 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11540015486230834038.vcf
14:31:38.047 INFO  Funcotator - ------------------------------------------------------------
14:31:38.047 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:38.047 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:38.047 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:38.047 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:38.047 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:38 PM GMT
14:31:38.047 INFO  Funcotator - ------------------------------------------------------------
14:31:38.047 INFO  Funcotator - ------------------------------------------------------------
14:31:38.047 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:38.047 INFO  Funcotator - Picard Version: 3.4.0
14:31:38.047 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:38.047 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:38.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:38.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:38.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:38.047 INFO  Funcotator - Deflater: IntelDeflater
14:31:38.047 INFO  Funcotator - Inflater: IntelInflater
14:31:38.047 INFO  Funcotator - GCS max retries/reopens: 20
14:31:38.047 INFO  Funcotator - Requester pays: disabled
14:31:38.047 INFO  Funcotator - Initializing engine
14:31:38.050 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
14:31:38.052 INFO  Funcotator - Done initializing engine
14:31:38.052 INFO  Funcotator - Validating sequence dictionaries...
14:31:38.052 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:38.052 INFO  Funcotator - Initializing data sources...
14:31:38.052 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:38.052 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:38.052 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:38.052 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:38.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:38.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:38.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:38.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:38.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:38.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:38.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:38.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:38.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:38.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:38.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:38.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:38.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:38.055 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:38.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:38.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:38.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:38.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:38.121 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:38.122 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:38.708 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:38.708 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:38.709 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:38.711 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:38.714 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:38.716 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:38.717 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:38.717 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:38.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:38.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:38.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:38.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:38.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:38.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:38.793 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:38.793 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:38.793 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:38.794 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:38.795 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:38.940 INFO  Funcotator - Initializing Funcotator Engine...
14:31:38.941 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:38.941 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:38.941 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator6910226563465265167.vcf
14:31:38.944 INFO  ProgressMeter - Starting traversal
14:31:38.945 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:38.993 INFO  ProgressMeter -             unmapped              0.0                     1           1250.0
14:31:38.993 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:38.993 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:38.994 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3084910592
14:31:38.995 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator6910226563465265167.vcf
14:31:39.096 INFO  Funcotator - ------------------------------------------------------------
14:31:39.096 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:39.096 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:39.096 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:39.096 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:39.096 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:39 PM GMT
14:31:39.096 INFO  Funcotator - ------------------------------------------------------------
14:31:39.096 INFO  Funcotator - ------------------------------------------------------------
14:31:39.096 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:39.096 INFO  Funcotator - Picard Version: 3.4.0
14:31:39.096 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:39.096 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:39.096 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:39.096 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:39.096 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:39.096 INFO  Funcotator - Deflater: IntelDeflater
14:31:39.096 INFO  Funcotator - Inflater: IntelInflater
14:31:39.096 INFO  Funcotator - GCS max retries/reopens: 20
14:31:39.096 INFO  Funcotator - Requester pays: disabled
14:31:39.096 INFO  Funcotator - Initializing engine
14:31:39.099 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
14:31:39.100 INFO  Funcotator - Done initializing engine
14:31:39.100 INFO  Funcotator - Validating sequence dictionaries...
14:31:39.100 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:39.100 INFO  Funcotator - Initializing data sources...
14:31:39.100 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:39.100 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:39.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:39.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:39.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:39.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:39.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:39.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:39.103 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:39.103 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:39.123 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:39.124 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:39.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:39.173 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:39.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:39.854 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:39.855 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:39.857 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:39.860 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:39.862 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:39.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:39.863 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:39.890 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:39.891 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:39.891 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:39.957 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:39.957 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:39.958 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:39.965 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:39.965 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:39.965 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:39.966 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:39.967 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:40.053 INFO  Funcotator - Initializing Funcotator Engine...
14:31:40.053 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:40.053 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:40.053 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator6955306609567394719.vcf
14:31:40.057 INFO  ProgressMeter - Starting traversal
14:31:40.057 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:40.064 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.103 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:31:40.106 INFO  ProgressMeter -             unmapped              0.0                     2           2449.0
14:31:40.106 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:31:40.106 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:40.106 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:40 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3154116608
14:31:40.107 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator6955306609567394719.vcf
14:31:40.198 INFO  Funcotator - ------------------------------------------------------------
14:31:40.198 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:40.198 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:40.198 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:40.198 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:40.198 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:40 PM GMT
14:31:40.198 INFO  Funcotator - ------------------------------------------------------------
14:31:40.198 INFO  Funcotator - ------------------------------------------------------------
14:31:40.198 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:40.199 INFO  Funcotator - Picard Version: 3.4.0
14:31:40.199 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:40.199 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:40.199 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:40.199 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:40.199 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:40.199 INFO  Funcotator - Deflater: IntelDeflater
14:31:40.199 INFO  Funcotator - Inflater: IntelInflater
14:31:40.199 INFO  Funcotator - GCS max retries/reopens: 20
14:31:40.199 INFO  Funcotator - Requester pays: disabled
14:31:40.199 INFO  Funcotator - Initializing engine
14:31:40.201 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
14:31:40.202 INFO  Funcotator - Done initializing engine
14:31:40.202 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:40.202 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:40.202 INFO  Funcotator - Initializing data sources...
14:31:40.202 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:40.202 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:40.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:40.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:40.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:40.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:40.204 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:40.204 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:40.205 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:40.224 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:40.224 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:40.313 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:40.313 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:40.936 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:40.936 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:40.937 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:40.939 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:40.942 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:40.944 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:40.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:40.945 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:41.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:41.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:41	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:41.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:41.072 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:41.072 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:41.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:41.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:41.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:41.080 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:41.081 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:41.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:41.169 INFO  Funcotator - Initializing Funcotator Engine...
14:31:41.169 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:41.169 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:41.169 INFO  FuncotatorUtils - Setting custom variant classification severities from: file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_order_for_int_test.tsv
14:31:41.170 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
14:31:41.170 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
14:31:41.170 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12788384484942316360.vcf
14:31:41.174 INFO  ProgressMeter - Starting traversal
14:31:41.174 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:41.207 INFO  ProgressMeter -             unmapped              0.0                     1           1818.2
14:31:41.207 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:41.207 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:41.208 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3229614080
14:31:41.209 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12788384484942316360.vcf
14:31:41.210 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_expected_out.vcf
[June 2, 2025 at 2:31:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
[June 2, 2025 at 2:31:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
14:31:41.648 INFO  Funcotator - ------------------------------------------------------------
14:31:41.648 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:41.648 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:41.648 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:41.648 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:41.648 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:41 PM GMT
14:31:41.648 INFO  Funcotator - ------------------------------------------------------------
14:31:41.648 INFO  Funcotator - ------------------------------------------------------------
14:31:41.648 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:41.648 INFO  Funcotator - Picard Version: 3.4.0
14:31:41.648 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:41.648 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:41.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:41.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:41.648 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:41.648 INFO  Funcotator - Deflater: IntelDeflater
14:31:41.648 INFO  Funcotator - Inflater: IntelInflater
14:31:41.648 INFO  Funcotator - GCS max retries/reopens: 20
14:31:41.649 INFO  Funcotator - Requester pays: disabled
14:31:41.649 INFO  Funcotator - Initializing engine
14:31:41.650 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:31:41.667 INFO  Funcotator - Done initializing engine
14:31:41.667 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:41.667 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:41.667 INFO  Funcotator - Initializing data sources...
14:31:41.667 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:41.667 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:41.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:41.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:41.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:41.668 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:41.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:41.668 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:41.669 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:41.669 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:41.669 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:41.670 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:41.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:41.679 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:41.688 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:41.697 INFO  Funcotator - Initializing Funcotator Engine...
14:31:41.703 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:41.704 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12641643104121977224.vcf
14:31:41.717 INFO  ProgressMeter - Starting traversal
14:31:41.717 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:41.745 INFO  ProgressMeter -             unmapped              0.0                   100         214285.7
14:31:41.745 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:31:41.745 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:41.751 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
14:31:41.752 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12641643104121977224.vcf
14:31:41.875 INFO  Funcotator - ------------------------------------------------------------
14:31:41.875 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:41.875 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:41.875 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:41.875 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:41.875 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:41 PM GMT
14:31:41.875 INFO  Funcotator - ------------------------------------------------------------
14:31:41.875 INFO  Funcotator - ------------------------------------------------------------
14:31:41.875 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:41.875 INFO  Funcotator - Picard Version: 3.4.0
14:31:41.875 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:41.875 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:41.875 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:41.875 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:41.875 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:41.875 INFO  Funcotator - Deflater: IntelDeflater
14:31:41.876 INFO  Funcotator - Inflater: IntelInflater
14:31:41.876 INFO  Funcotator - GCS max retries/reopens: 20
14:31:41.876 INFO  Funcotator - Requester pays: disabled
14:31:41.876 INFO  Funcotator - Initializing engine
14:31:41.878 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
14:31:41.880 INFO  Funcotator - Done initializing engine
14:31:41.880 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:41.880 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:41.880 INFO  Funcotator - Initializing data sources...
14:31:41.880 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/
14:31:41.880 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:41.880 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
14:31:41.880 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:41.880 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:41.880 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:41.881 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
14:31:41.881 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:31:41.881 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
14:31:41.884 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
14:31:41.887 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/dbSnp/hg19/dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
14:31:41.889 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:41.889 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:41.890 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:41.890 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:41.891 INFO  Funcotator - Initializing Funcotator Engine...
14:31:41.891 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:41.891 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:41.891 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:41.891 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing11556262193502842003.vcf
14:31:41.894 INFO  ProgressMeter - Starting traversal
14:31:41.894 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:41.916 INFO  ProgressMeter -             unmapped              0.0                     1           2727.3
14:31:41.916 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:41.916 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
14:31:41.919 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
14:31:41.920 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing11556262193502842003.vcf
14:31:42.023 INFO  Funcotator - ------------------------------------------------------------
14:31:42.023 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:42.023 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:42.023 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:42.023 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:42.023 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:42 PM GMT
14:31:42.023 INFO  Funcotator - ------------------------------------------------------------
14:31:42.023 INFO  Funcotator - ------------------------------------------------------------
14:31:42.023 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:42.023 INFO  Funcotator - Picard Version: 3.4.0
14:31:42.023 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:42.023 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:42.023 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:42.023 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:42.023 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:42.023 INFO  Funcotator - Deflater: IntelDeflater
14:31:42.023 INFO  Funcotator - Inflater: IntelInflater
14:31:42.023 INFO  Funcotator - GCS max retries/reopens: 20
14:31:42.023 INFO  Funcotator - Requester pays: disabled
14:31:42.023 INFO  Funcotator - Initializing engine
14:31:42.024 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:31:42.025 INFO  Funcotator - Done initializing engine
14:31:42.025 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:42.025 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:42.025 INFO  Funcotator - Initializing data sources...
14:31:42.025 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:42.025 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:42.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:42.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:42.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:42.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:42.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:42.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:42.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:42.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:42.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:42.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:42.028 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:42.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:42.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:42.047 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:42.048 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:42.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:42.108 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:42.760 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:42.760 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:42.761 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:42.763 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:42.766 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:42.768 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:42.768 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:42.769 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:42.796 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:42.796 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:42	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:42.797 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:42.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:42.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:42.837 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:42.845 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:42.845 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:42.845 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:42.846 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:42.846 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:42.935 INFO  Funcotator - Initializing Funcotator Engine...
14:31:42.935 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:42.935 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:31:42.935 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:31:42.935 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:31:42.935 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:31:42.936 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:31:42.936 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:42.936 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6830068297732898190.vcf
14:31:42.936 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:42.938 INFO  ProgressMeter - Starting traversal
14:31:42.938 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:42.960 INFO  ProgressMeter -             unmapped              0.0                     3           8181.8
14:31:42.960 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:31:42.960 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:42.963 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3003121664
14:31:43.055 INFO  Funcotator - ------------------------------------------------------------
14:31:43.055 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:43.055 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:43.055 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:43.055 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:43.055 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:43 PM GMT
14:31:43.055 INFO  Funcotator - ------------------------------------------------------------
14:31:43.055 INFO  Funcotator - ------------------------------------------------------------
14:31:43.055 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:43.055 INFO  Funcotator - Picard Version: 3.4.0
14:31:43.055 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:43.055 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:43.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:43.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:43.055 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:43.055 INFO  Funcotator - Deflater: IntelDeflater
14:31:43.055 INFO  Funcotator - Inflater: IntelInflater
14:31:43.055 INFO  Funcotator - GCS max retries/reopens: 20
14:31:43.055 INFO  Funcotator - Requester pays: disabled
14:31:43.055 INFO  Funcotator - Initializing engine
14:31:43.056 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:31:43.057 INFO  Funcotator - Done initializing engine
14:31:43.057 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:43.057 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:43.057 INFO  Funcotator - Initializing data sources...
14:31:43.057 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:43.057 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:43.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:43.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:43.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:43.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:43.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:43.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:43.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:43.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:43.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:43.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:43.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:43.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:43.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:43.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:43.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:43.060 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:43.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:43.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:43.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:43.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:43.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:43.127 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:43.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:43.785 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:43.787 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:43.790 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:43.793 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:43.795 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:43.795 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:43.796 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:43.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:43.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:43.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:43.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:43.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:43.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:43.870 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:43.870 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:43.871 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:43.871 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:43.872 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:43.955 INFO  Funcotator - Initializing Funcotator Engine...
14:31:43.956 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:43.956 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:43.956 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9821060286485599247.vcf
14:31:43.957 INFO  ProgressMeter - Starting traversal
14:31:43.957 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:44.115 INFO  ProgressMeter -             unmapped              0.0                     4           1528.7
14:31:44.115 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:44.115 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:44.115 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3003121664
14:31:44.210 INFO  Funcotator - ------------------------------------------------------------
14:31:44.210 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:44.210 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:44.210 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:44.210 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:44.210 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:44 PM GMT
14:31:44.210 INFO  Funcotator - ------------------------------------------------------------
14:31:44.210 INFO  Funcotator - ------------------------------------------------------------
14:31:44.210 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:44.210 INFO  Funcotator - Picard Version: 3.4.0
14:31:44.210 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:44.210 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:44.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:44.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:44.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:44.210 INFO  Funcotator - Deflater: IntelDeflater
14:31:44.210 INFO  Funcotator - Inflater: IntelInflater
14:31:44.210 INFO  Funcotator - GCS max retries/reopens: 20
14:31:44.210 INFO  Funcotator - Requester pays: disabled
14:31:44.210 INFO  Funcotator - Initializing engine
14:31:44.211 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:31:44.212 INFO  Funcotator - Done initializing engine
14:31:44.212 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:44.212 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:44.212 INFO  Funcotator - Initializing data sources...
14:31:44.212 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:44.212 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:44.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:44.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:44.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:44.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:44.214 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:44.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:44.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:44.234 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:44.234 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:44.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:44.281 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:44.898 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:44.899 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:44.900 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:44.902 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:44.904 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:44.907 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:44.907 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:44.907 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:44.935 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:44.935 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:44.935 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:44.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:44.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:44.976 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:44.988 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:44.989 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:44.989 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:44.990 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:44.990 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:45.078 INFO  Funcotator - Initializing Funcotator Engine...
14:31:45.078 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:45.079 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:31:45.079 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:31:45.079 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:31:45.079 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:31:45.079 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:45.079 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10146062031408276502.vcf
14:31:45.080 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:45.081 INFO  ProgressMeter - Starting traversal
14:31:45.081 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:45.100 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
14:31:45.100 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:31:45.100 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:45.103 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3003121664
14:31:45.198 INFO  Funcotator - ------------------------------------------------------------
14:31:45.198 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:45.198 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:45.198 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:45.198 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:45.198 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:45 PM GMT
14:31:45.198 INFO  Funcotator - ------------------------------------------------------------
14:31:45.198 INFO  Funcotator - ------------------------------------------------------------
14:31:45.198 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:45.198 INFO  Funcotator - Picard Version: 3.4.0
14:31:45.198 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:45.198 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:45.198 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:45.198 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:45.198 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:45.198 INFO  Funcotator - Deflater: IntelDeflater
14:31:45.198 INFO  Funcotator - Inflater: IntelInflater
14:31:45.198 INFO  Funcotator - GCS max retries/reopens: 20
14:31:45.198 INFO  Funcotator - Requester pays: disabled
14:31:45.198 INFO  Funcotator - Initializing engine
14:31:45.199 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:31:45.200 INFO  Funcotator - Done initializing engine
14:31:45.200 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:45.200 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:45.200 INFO  Funcotator - Initializing data sources...
14:31:45.200 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:45.200 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:45.200 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:45.200 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:45.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:45.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:45.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:45.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:45.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:45.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:45.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:45.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:45.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:45.203 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:45.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:45.228 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:45.228 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:45.273 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:45.274 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:45.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:45.852 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:45.853 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:45.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:45.858 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:45.860 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:45.860 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:45.861 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:45.888 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:45.888 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:45.889 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:45.927 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:45.927 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:45.928 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:45.991 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:45.991 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:45.991 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:45.992 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:45.992 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:46.078 INFO  Funcotator - Initializing Funcotator Engine...
14:31:46.078 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:46.078 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:46.078 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10103943186694315872.vcf
14:31:46.079 INFO  ProgressMeter - Starting traversal
14:31:46.079 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:46.182 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
14:31:46.182 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:46.182 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:46.183 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3003121664
14:31:46.273 INFO  Funcotator - ------------------------------------------------------------
14:31:46.273 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:46.273 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:46.273 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:46.273 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:46.273 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:46 PM GMT
14:31:46.273 INFO  Funcotator - ------------------------------------------------------------
14:31:46.273 INFO  Funcotator - ------------------------------------------------------------
14:31:46.274 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:46.274 INFO  Funcotator - Picard Version: 3.4.0
14:31:46.274 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:46.274 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:46.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:46.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:46.274 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:46.274 INFO  Funcotator - Deflater: IntelDeflater
14:31:46.274 INFO  Funcotator - Inflater: IntelInflater
14:31:46.274 INFO  Funcotator - GCS max retries/reopens: 20
14:31:46.274 INFO  Funcotator - Requester pays: disabled
14:31:46.274 INFO  Funcotator - Initializing engine
14:31:46.275 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:31:46.276 INFO  Funcotator - Done initializing engine
14:31:46.276 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:46.276 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:46.276 INFO  Funcotator - Initializing data sources...
14:31:46.276 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:46.276 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:46.276 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:46.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:46.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:46.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:46.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:46.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:46.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:46.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:46.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:46.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:46.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:46.279 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:46.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:46.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:46.303 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:46.348 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:46.349 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:47.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:47.071 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:47.072 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:47.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:47.077 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:47.079 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:47.079 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:47.080 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:47.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:47.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:47.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:47.146 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:47.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:47.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:47.154 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:47.155 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:47.155 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:47.156 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:47.156 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:47.243 INFO  Funcotator - Initializing Funcotator Engine...
14:31:47.243 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:47.243 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:31:47.243 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:31:47.243 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:31:47.243 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:31:47.244 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:31:47.244 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:47.244 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6280150315324939466.maf
14:31:47.244 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:47.245 INFO  ProgressMeter - Starting traversal
14:31:47.245 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:47.270 INFO  ProgressMeter -             unmapped              0.0                     3           7200.0
14:31:47.270 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:31:47.270 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:47.270 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3244294144
14:31:47.371 INFO  Funcotator - ------------------------------------------------------------
14:31:47.371 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:47.371 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:47.371 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:47.371 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:47.371 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:47 PM GMT
14:31:47.371 INFO  Funcotator - ------------------------------------------------------------
14:31:47.371 INFO  Funcotator - ------------------------------------------------------------
14:31:47.371 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:47.372 INFO  Funcotator - Picard Version: 3.4.0
14:31:47.372 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:47.372 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:47.372 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:47.372 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:47.372 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:47.372 INFO  Funcotator - Deflater: IntelDeflater
14:31:47.372 INFO  Funcotator - Inflater: IntelInflater
14:31:47.372 INFO  Funcotator - GCS max retries/reopens: 20
14:31:47.372 INFO  Funcotator - Requester pays: disabled
14:31:47.372 INFO  Funcotator - Initializing engine
14:31:47.372 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:31:47.373 INFO  Funcotator - Done initializing engine
14:31:47.373 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:47.373 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:47.373 INFO  Funcotator - Initializing data sources...
14:31:47.373 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:47.373 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:47.373 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:47.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:47.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:47.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:47.376 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:47.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:47.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:47.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:47.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:47.441 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:47.441 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:48.033 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:48.033 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:48.034 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:48.036 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:48.039 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:48.041 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:48.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:48.042 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:48.069 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:48.069 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:48.070 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:48.108 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:48.108 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:48.108 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:48.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:48.116 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:48.116 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:48.116 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:48.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:48.199 INFO  Funcotator - Initializing Funcotator Engine...
14:31:48.199 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:48.199 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:48.199 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14796904253858399701.maf
14:31:48.200 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:48.201 INFO  ProgressMeter - Starting traversal
14:31:48.201 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:48.309 INFO  ProgressMeter -             unmapped              0.0                     4           2222.2
14:31:48.309 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:48.309 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:48.309 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:48 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3244294144
14:31:48.401 INFO  Funcotator - ------------------------------------------------------------
14:31:48.401 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:48.401 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:48.401 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:48.401 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:48.401 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:48 PM GMT
14:31:48.401 INFO  Funcotator - ------------------------------------------------------------
14:31:48.401 INFO  Funcotator - ------------------------------------------------------------
14:31:48.401 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:48.401 INFO  Funcotator - Picard Version: 3.4.0
14:31:48.401 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:48.401 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:48.401 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:48.401 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:48.401 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:48.401 INFO  Funcotator - Deflater: IntelDeflater
14:31:48.401 INFO  Funcotator - Inflater: IntelInflater
14:31:48.401 INFO  Funcotator - GCS max retries/reopens: 20
14:31:48.401 INFO  Funcotator - Requester pays: disabled
14:31:48.401 INFO  Funcotator - Initializing engine
14:31:48.402 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:31:48.403 INFO  Funcotator - Done initializing engine
14:31:48.403 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:48.403 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:48.403 INFO  Funcotator - Initializing data sources...
14:31:48.403 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:48.403 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:48.403 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:48.403 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:48.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:48.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:48.405 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:48.406 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:48.406 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:48.425 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:48.426 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:48.471 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:48.471 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:49.050 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.050 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:49.051 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.055 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.058 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:49.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:49.058 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:49.086 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:49.086 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:49.086 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:49.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:49.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:49.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:49.134 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:49.134 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:49.134 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:49.135 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:49.135 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:49.222 INFO  Funcotator - Initializing Funcotator Engine...
14:31:49.222 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:31:49.222 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:31:49.222 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:31:49.222 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:31:49.222 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:31:49.222 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:31:49.222 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:31:49.223 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:31:49.223 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:49.223 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5098261534796804766.maf
14:31:49.223 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:49.224 INFO  ProgressMeter - Starting traversal
14:31:49.224 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:49.242 INFO  ProgressMeter -             unmapped              0.0                     3          10000.0
14:31:49.243 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:31:49.243 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:49.243 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:49 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3244294144
14:31:49.331 INFO  Funcotator - ------------------------------------------------------------
14:31:49.331 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:49.331 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:49.331 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:49.331 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:49.331 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:49 PM GMT
14:31:49.331 INFO  Funcotator - ------------------------------------------------------------
14:31:49.331 INFO  Funcotator - ------------------------------------------------------------
14:31:49.331 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:49.331 INFO  Funcotator - Picard Version: 3.4.0
14:31:49.331 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:49.331 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:49.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:49.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:49.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:49.331 INFO  Funcotator - Deflater: IntelDeflater
14:31:49.331 INFO  Funcotator - Inflater: IntelInflater
14:31:49.331 INFO  Funcotator - GCS max retries/reopens: 20
14:31:49.331 INFO  Funcotator - Requester pays: disabled
14:31:49.331 INFO  Funcotator - Initializing engine
14:31:49.332 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:31:49.333 INFO  Funcotator - Done initializing engine
14:31:49.333 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:49.333 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:49.333 INFO  Funcotator - Initializing data sources...
14:31:49.333 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:49.333 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:49.333 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:49.333 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:49.333 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:49.333 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:49.334 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:49.334 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:49.334 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.334 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:49.334 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:49.335 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:49.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:49.336 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:49.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:49.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:49.400 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:49.401 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:49.952 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.952 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:49.953 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.956 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.958 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:49.960 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:49.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:49.961 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:49.988 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:49.989 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:49.989 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:50.083 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:50.083 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:50.084 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:50.090 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:50.091 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:50.091 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.092 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:50.092 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:50.175 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.176 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:50.176 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:50.176 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5181013836881474305.maf
14:31:50.176 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:50.176 INFO  ProgressMeter - Starting traversal
14:31:50.176 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.278 INFO  ProgressMeter -             unmapped              0.0                     4           2352.9
14:31:50.278 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:31:50.278 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:31:50.278 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3244294144
14:31:50.370 INFO  Funcotator - ------------------------------------------------------------
14:31:50.370 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:50.370 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:50.370 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:50.370 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:50.370 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:50 PM GMT
14:31:50.370 INFO  Funcotator - ------------------------------------------------------------
14:31:50.370 INFO  Funcotator - ------------------------------------------------------------
14:31:50.370 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:50.370 INFO  Funcotator - Picard Version: 3.4.0
14:31:50.370 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:50.370 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:50.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:50.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:50.370 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:50.370 INFO  Funcotator - Deflater: IntelDeflater
14:31:50.370 INFO  Funcotator - Inflater: IntelInflater
14:31:50.370 INFO  Funcotator - GCS max retries/reopens: 20
14:31:50.370 INFO  Funcotator - Requester pays: disabled
14:31:50.370 INFO  Funcotator - Initializing engine
14:31:50.371 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:31:50.395 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:31:50.395 INFO  Funcotator - Done initializing engine
14:31:50.395 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:50.395 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:50.395 INFO  Funcotator - Initializing data sources...
14:31:50.395 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
14:31:50.395 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:50.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
14:31:50.396 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:50.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.396 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:50.398 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.407 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.415 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.423 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.423 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.424 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.424 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
14:31:50.425 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.429 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:50.429 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8668419681431131698.vcf
14:31:50.442 INFO  ProgressMeter - Starting traversal
14:31:50.442 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.454 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
14:31:50.454 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:31:50.454 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:50.461 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:50.553 INFO  Funcotator - ------------------------------------------------------------
14:31:50.553 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:50.553 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:50.553 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:50.553 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:50.553 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:50 PM GMT
14:31:50.553 INFO  Funcotator - ------------------------------------------------------------
14:31:50.553 INFO  Funcotator - ------------------------------------------------------------
14:31:50.553 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:50.553 INFO  Funcotator - Picard Version: 3.4.0
14:31:50.553 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:50.553 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:50.553 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:50.553 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:50.553 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:50.553 INFO  Funcotator - Deflater: IntelDeflater
14:31:50.553 INFO  Funcotator - Inflater: IntelInflater
14:31:50.553 INFO  Funcotator - GCS max retries/reopens: 20
14:31:50.553 INFO  Funcotator - Requester pays: disabled
14:31:50.553 INFO  Funcotator - Initializing engine
14:31:50.554 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:31:50.575 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:31:50.575 INFO  Funcotator - Done initializing engine
14:31:50.575 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:50.575 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:50.575 INFO  Funcotator - Initializing data sources...
14:31:50.575 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
14:31:50.575 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:50.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
14:31:50.576 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:50.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.576 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:50.577 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.585 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.593 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:50.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.601 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.601 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
14:31:50.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v43.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/gencode_pik3ca/hg38/gencode.v43.PIK3CA_transcript.fasta
14:31:50.602 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.606 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:50.606 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5908229315543358148.vcf
14:31:50.618 INFO  ProgressMeter - Starting traversal
14:31:50.618 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.629 INFO  ProgressMeter -             unmapped              0.0                    32         174545.5
14:31:50.629 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:31:50.629 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:50.634 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:50.635 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8668419681431131698.vcf
14:31:50.644 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out5908229315543358148.vcf
14:31:50.743 INFO  Funcotator - ------------------------------------------------------------
14:31:50.743 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:50.743 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:50.743 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:50.743 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:50.743 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:50 PM GMT
14:31:50.743 INFO  Funcotator - ------------------------------------------------------------
14:31:50.743 INFO  Funcotator - ------------------------------------------------------------
14:31:50.743 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:50.743 INFO  Funcotator - Picard Version: 3.4.0
14:31:50.743 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:50.743 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:50.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:50.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:50.743 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:50.743 INFO  Funcotator - Deflater: IntelDeflater
14:31:50.743 INFO  Funcotator - Inflater: IntelInflater
14:31:50.743 INFO  Funcotator - GCS max retries/reopens: 20
14:31:50.743 INFO  Funcotator - Requester pays: disabled
14:31:50.743 INFO  Funcotator - Initializing engine
14:31:50.744 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
14:31:50.745 INFO  Funcotator - Done initializing engine
14:31:50.745 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:50.745 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:50.745 INFO  Funcotator - Initializing data sources...
14:31:50.745 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:50.745 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:50.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.746 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.746 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:50.746 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.746 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.746 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.747 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:50.747 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.748 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.749 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.750 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.750 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:50.750 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:50.750 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11939202648516682635.maf
14:31:50.751 INFO  ProgressMeter - Starting traversal
14:31:50.751 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.752 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[NORMAL T*/T* AD 43,1 {AF=0.026, ALT_F1R2=0, ALT_F2R1=1, FOXOG=0.00, QSS=1450,32, REF_F1R2=29, REF_F2R1=14}],[TUMOR T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
14:31:50.753 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[NORMAL TGCGAA*/TGCGAA* AD 45,1 {AF=0.026, QSS=1503,32}],[TUMOR TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
14:31:50.753 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[NORMAL G*/G* AD 145,4 {AF=0.028, ALT_F1R2=0, ALT_F2R1=4, FOXOG=0.00, QSS=5064,124, REF_F1R2=72, REF_F2R1=73}],[TUMOR G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
14:31:50.755 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[NORMAL T*/T* AD 22,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=799,0, REF_F1R2=12, REF_F2R1=10}],[TUMOR T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
14:31:50.755 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[NORMAL A*/A* AD 45,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=1560,0, REF_F1R2=20, REF_F2R1=25}],[TUMOR A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
14:31:50.756 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[NORMAL G*/G* AD 13,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=378,0, REF_F1R2=8, REF_F2R1=5}],[TUMOR G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
14:31:50.756 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:31:50.756 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:31:50.756 WARN  Funcotator - ================================================================================
14:31:50.756 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:31:50.756 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:31:50.756 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:31:50.756 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:31:50.756 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:31:50.756 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:31:50.756 WARN  Funcotator - --------------------------------------------------------------------------------
14:31:50.756 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:31:50.756 WARN  Funcotator -  run was misconfigured.     
14:31:50.756 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:31:50.756 WARN  Funcotator - ================================================================================
14:31:50.756 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:50.756 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:50.846 INFO  Funcotator - ------------------------------------------------------------
14:31:50.846 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:50.846 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:50.846 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:50.846 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:50.846 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:50 PM GMT
14:31:50.846 INFO  Funcotator - ------------------------------------------------------------
14:31:50.846 INFO  Funcotator - ------------------------------------------------------------
14:31:50.846 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:50.846 INFO  Funcotator - Picard Version: 3.4.0
14:31:50.846 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:50.846 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:50.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:50.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:50.846 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:50.846 INFO  Funcotator - Deflater: IntelDeflater
14:31:50.846 INFO  Funcotator - Inflater: IntelInflater
14:31:50.846 INFO  Funcotator - GCS max retries/reopens: 20
14:31:50.846 INFO  Funcotator - Requester pays: disabled
14:31:50.846 INFO  Funcotator - Initializing engine
14:31:50.847 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
14:31:50.848 INFO  Funcotator - Done initializing engine
14:31:50.848 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:50.848 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:50.848 INFO  Funcotator - Initializing data sources...
14:31:50.848 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:50.848 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:50.848 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.849 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.849 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.849 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:50.849 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.849 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.849 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.850 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.850 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.850 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:50.851 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.851 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.853 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.853 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.853 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:50.853 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:50.853 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13632337879444909423.maf
14:31:50.854 INFO  ProgressMeter - Starting traversal
14:31:50.854 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.855 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 @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[SM-74NEG T*/T* AD 43,1 {AF=0.026, ALT_F1R2=0, ALT_F2R1=1, FOXOG=0.00, QSS=1450,32, REF_F1R2=29, REF_F2R1=14}],[SM-74P4M T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
14:31:50.856 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 @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[SM-74NEG TGCGAA*/TGCGAA* AD 45,1 {AF=0.026, QSS=1503,32}],[SM-74P4M TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
14:31:50.856 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 @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[SM-74NEG G*/G* AD 145,4 {AF=0.028, ALT_F1R2=0, ALT_F2R1=4, FOXOG=0.00, QSS=5064,124, REF_F1R2=72, REF_F2R1=73}],[SM-74P4M G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
14:31:50.857 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[SM-74NEG T*/T* AD 22,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=799,0, REF_F1R2=12, REF_F2R1=10}],[SM-74P4M T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
14:31:50.858 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[SM-74NEG A*/A* AD 45,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=1560,0, REF_F1R2=20, REF_F2R1=25}],[SM-74P4M A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
14:31:50.859 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[SM-74NEG G*/G* AD 13,0 {AF=0.00, ALT_F1R2=0, ALT_F2R1=0, FOXOG=NaN, QSS=378,0, REF_F1R2=8, REF_F2R1=5}],[SM-74P4M G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
14:31:50.859 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:31:50.859 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:31:50.859 WARN  Funcotator - ================================================================================
14:31:50.859 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:31:50.859 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:31:50.859 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:31:50.859 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:31:50.859 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:31:50.859 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:31:50.859 WARN  Funcotator - --------------------------------------------------------------------------------
14:31:50.859 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:31:50.859 WARN  Funcotator -  run was misconfigured.     
14:31:50.859 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:31:50.859 WARN  Funcotator - ================================================================================
14:31:50.859 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:50.859 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:50.955 INFO  Funcotator - ------------------------------------------------------------
14:31:50.955 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:50.955 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:50.955 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:50.955 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:50.955 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:50 PM GMT
14:31:50.955 INFO  Funcotator - ------------------------------------------------------------
14:31:50.955 INFO  Funcotator - ------------------------------------------------------------
14:31:50.955 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:50.955 INFO  Funcotator - Picard Version: 3.4.0
14:31:50.955 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:50.955 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:50.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:50.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:50.955 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:50.955 INFO  Funcotator - Deflater: IntelDeflater
14:31:50.955 INFO  Funcotator - Inflater: IntelInflater
14:31:50.955 INFO  Funcotator - GCS max retries/reopens: 20
14:31:50.955 INFO  Funcotator - Requester pays: disabled
14:31:50.955 INFO  Funcotator - Initializing engine
14:31:50.957 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf
14:31:50.958 INFO  Funcotator - Done initializing engine
14:31:50.958 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:50.958 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:50.958 INFO  Funcotator - Initializing data sources...
14:31:50.958 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:50.958 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:50.958 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.958 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.958 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.958 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:50.958 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.958 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:50.959 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:50.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:50.959 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.959 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:50.960 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.961 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.962 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:50.962 INFO  Funcotator - Initializing Funcotator Engine...
14:31:50.963 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:50.963 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:50.963 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11380108328261082827.maf
14:31:50.963 INFO  ProgressMeter - Starting traversal
14:31:50.963 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:50.964 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[TUMOR T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
14:31:50.965 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[TUMOR TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
14:31:50.965 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[TUMOR G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
14:31:50.966 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[TUMOR T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
14:31:50.967 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[TUMOR A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
14:31:50.968 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[TUMOR G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
14:31:50.968 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:31:50.968 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:31:50.968 WARN  Funcotator - ================================================================================
14:31:50.968 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:31:50.968 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:31:50.968 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:31:50.968 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:31:50.968 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:31:50.968 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:31:50.968 WARN  Funcotator - --------------------------------------------------------------------------------
14:31:50.968 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:31:50.968 WARN  Funcotator -  run was misconfigured.     
14:31:50.968 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:31:50.968 WARN  Funcotator - ================================================================================
14:31:50.968 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:50.968 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.058 INFO  Funcotator - ------------------------------------------------------------
14:31:51.058 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.058 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.058 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.058 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.058 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.058 INFO  Funcotator - ------------------------------------------------------------
14:31:51.058 INFO  Funcotator - ------------------------------------------------------------
14:31:51.058 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.058 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.058 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.058 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.058 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.058 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.058 INFO  Funcotator - Inflater: IntelInflater
14:31:51.058 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.058 INFO  Funcotator - Requester pays: disabled
14:31:51.058 INFO  Funcotator - Initializing engine
14:31:51.060 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf
14:31:51.060 INFO  Funcotator - Done initializing engine
14:31:51.060 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:51.060 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:51.060 INFO  Funcotator - Initializing data sources...
14:31:51.060 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:51.060 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:51.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.061 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:51.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.061 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:51.062 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.062 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:51.063 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.065 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.065 INFO  Funcotator - Initializing Funcotator Engine...
14:31:51.065 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:51.065 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:51.066 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13123565389389907613.maf
14:31:51.066 INFO  ProgressMeter - Starting traversal
14:31:51.066 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:51.067 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 Q. of type=SNP alleles=[T*, C] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=8.06, TLOD=7.01} GT=[[SM-74P4M T*/C AD 42,3 {AF=0.075, ALT_F1R2=0, ALT_F2R1=3, FOXOG=0.00, QSS=1442,107, REF_F1R2=21, REF_F2R1=21}]] filters=clustered_events,multi_event_alt_allele_in_normal
14:31:51.068 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 Q. of type=INDEL alleles=[TGCGAA*, T] attr={DB=true, ECNT=2, HCNT=4, MAX_ED=10, MIN_ED=10, NLOD=7.23, TLOD=5.53} GT=[[SM-74P4M TGCGAA*/T AD 44,2 {AF=0.049, QSS=1531,75}]] filters=clustered_events,multi_event_alt_allele_in_normal,t_lod_fstar
14:31:51.068 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 Q. of type=SNP alleles=[G*, A] attr={ECNT=1, HCNT=3, MAX_ED=., MIN_ED=., NLOD=28.04, TLOD=6.77} GT=[[SM-74P4M G*/A AD 117,4 {AF=0.034, ALT_F1R2=2, ALT_F2R1=2, FOXOG=0.500, QSS=4020,132, REF_F1R2=60, REF_F2R1=57}]] filters=alt_allele_in_normal
14:31:51.070 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 Q. of type=SNP alleles=[T*, A] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=5.42, TLOD=14.08} GT=[[SM-74P4M T*/A AD 16,6 {AF=0.278, ALT_F1R2=4, ALT_F2R1=2, FOXOG=0.667, QSS=548,199, REF_F1R2=8, REF_F2R1=8}]] filters=
14:31:51.070 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 Q. of type=SNP alleles=[A*, G] attr={ECNT=1, HCNT=2, MAX_ED=., MIN_ED=., NLOD=10.53, TLOD=19.03} GT=[[SM-74P4M A*/G AD 24,8 {AF=0.259, ALT_F1R2=3, ALT_F2R1=5, FOXOG=0.375, QSS=846,255, REF_F1R2=9, REF_F2R1=15}]] filters=
14:31:51.072 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 Q. of type=SNP alleles=[G*, C] attr={ECNT=1, HCNT=1, MAX_ED=., MIN_ED=., NLOD=3.26, TLOD=11.67} GT=[[SM-74P4M G*/C AD 23,7 {AF=0.190, ALT_F1R2=3, ALT_F2R1=4, FOXOG=0.429, QSS=668,207, REF_F1R2=7, REF_F2R1=16}]] filters=
14:31:51.072 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
14:31:51.072 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:31:51.072 WARN  Funcotator - ================================================================================
14:31:51.072 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:31:51.072 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:31:51.072 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:31:51.072 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:31:51.072 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:31:51.072 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:31:51.072 WARN  Funcotator - --------------------------------------------------------------------------------
14:31:51.072 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:31:51.072 WARN  Funcotator -  run was misconfigured.     
14:31:51.072 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:31:51.072 WARN  Funcotator - ================================================================================
14:31:51.072 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:51.072 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.173 INFO  Funcotator - ------------------------------------------------------------
14:31:51.173 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.173 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.173 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.173 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.173 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.173 INFO  Funcotator - ------------------------------------------------------------
14:31:51.173 INFO  Funcotator - ------------------------------------------------------------
14:31:51.173 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.173 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.173 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.173 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.173 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.173 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.173 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.173 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.173 INFO  Funcotator - Inflater: IntelInflater
14:31:51.173 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.173 INFO  Funcotator - Requester pays: disabled
14:31:51.173 INFO  Funcotator - Initializing engine
14:31:51.174 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:31:51.175 INFO  Funcotator - Done initializing engine
14:31:51.175 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:51.175 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:51.175 INFO  Funcotator - Initializing data sources...
14:31:51.175 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:51.175 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:51.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.175 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:51.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.175 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:51.176 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.176 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.176 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.177 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:51.177 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.178 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.179 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.179 INFO  Funcotator - Initializing Funcotator Engine...
14:31:51.179 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:51.179 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:51.180 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7430843508800861607.vcf
14:31:51.183 INFO  ProgressMeter - Starting traversal
14:31:51.183 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:51.192 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
14:31:51.192 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:31:51.192 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:31:51.194 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.195 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7430843508800861607.vcf
14:31:51.287 INFO  Funcotator - ------------------------------------------------------------
14:31:51.287 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.287 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.287 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.287 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.287 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.287 INFO  Funcotator - ------------------------------------------------------------
14:31:51.287 INFO  Funcotator - ------------------------------------------------------------
14:31:51.287 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.287 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.287 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.287 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.287 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.287 INFO  Funcotator - Inflater: IntelInflater
14:31:51.287 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.287 INFO  Funcotator - Requester pays: disabled
14:31:51.287 INFO  Funcotator - Initializing engine
14:31:51.288 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
14:31:51.289 INFO  Funcotator - Done initializing engine
14:31:51.289 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:51.289 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:51.289 INFO  Funcotator - Initializing data sources...
14:31:51.289 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:51.289 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:51.289 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.289 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.289 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.289 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:51.289 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.289 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:51.290 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:51.290 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:51.290 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.291 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:51.291 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.292 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.293 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:51.294 INFO  Funcotator - Initializing Funcotator Engine...
14:31:51.294 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:51.294 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:51.294 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13283359284721464437.maf
14:31:51.294 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:51.294 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.385 INFO  Funcotator - ------------------------------------------------------------
14:31:51.385 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.385 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.385 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.385 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.385 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.385 INFO  Funcotator - ------------------------------------------------------------
14:31:51.385 INFO  Funcotator - ------------------------------------------------------------
14:31:51.385 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.385 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.385 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.385 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.385 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.385 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.385 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.385 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.385 INFO  Funcotator - Inflater: IntelInflater
14:31:51.385 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.385 INFO  Funcotator - Requester pays: disabled
14:31:51.385 INFO  Funcotator - Initializing engine
14:31:51.386 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
14:31:51.399 INFO  Funcotator - Done initializing engine
14:31:51.399 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:51.399 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:51.399 INFO  Funcotator - Initializing data sources...
14:31:51.399 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:51.399 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:51.399 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:51.399 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:51.399 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:51.399 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:51.399 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:51.399 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:51.400 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:31:51.400 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:31:51.401 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:51.401 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:51.401 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:51.409 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:51.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:31:51.427 INFO  Funcotator - Initializing Funcotator Engine...
14:31:51.434 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:51.434 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1124920647411227269.maf
14:31:51.434 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:51.435 INFO  ProgressMeter - Starting traversal
14:31:51.435 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:51.437 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
14:31:51.437 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != C reference coding seq) @[chr3:179199000]!  Substituting given allele for sequence code (CAT->AAT)
14:31:51.437 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.438 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:51.438 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:31:51.438 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:31:51.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199000 Q308.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-1.052e+00, ClippingRankSum=-1.910e-01, DP=82, ExcessHet=4.7712, FS=24.798, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=34.33, MQRankSum=-2.200e+00, QD=6.43, ReadPosRankSum=-9.570e-01, SOR=2.422, VQSLOD=-1.252e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:13,0,0:13:0:.:.:0,0,146,0,146,146	0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886	0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.442 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.443 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:51.443 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:31:51.443 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:31:51.443 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199001 Q308.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-1.339e+00, ClippingRankSum=0.00, DP=82, ExcessHet=4.7712, FS=24.798, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=34.33, MQRankSum=-2.200e+00, QD=6.43, ReadPosRankSum=-1.148e+00, SOR=2.422, VQSLOD=-1.254e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:13,0,0:13:0:.:.:0,0,146,0,146,146	0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886	0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.443 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
14:31:51.444 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref A != T reference coding seq) @[chr3:179199002]!  Substituting given allele for sequence code (CAT->CAA)
14:31:51.444 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.444 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:51.444 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:31:51.444 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:31:51.444 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199002 Q194.52 of type=SNP alleles=[A*, *, C] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-2.991e+00, ClippingRankSum=-4.900e-02, DP=106, ExcessHet=4.7712, FS=16.473, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=37.30, MQRankSum=-1.470e-01, QD=2.95, ReadPosRankSum=-7.360e-01, SOR=1.435, VQSLOD=-9.044e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:15,0,0:15:0:.:.:0,0,273,0,273,273	0/1:23,7,0:30:49:.:.:49,0,658,118,678,796	0/2:30,0,6:36:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:160,252,1513,0,1261,1243 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.444 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
14:31:51.445 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = A, ref G != C reference coding seq) @[chr3:179199003]!  Substituting given allele for sequence code (CAA->GAA)
14:31:51.445 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:31:51.445 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:31:51.445 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:31:51.445 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:31:51.445 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199003 Q1706.05 of type=SNP alleles=[G*, *, A] attr={AC=[2, 2], AF=[0.500, 0.500], AN=4, DB=true, DP=76, ExcessHet=3.0103, FS=0.000, MLEAC=[2, 2], MLEAF=[0.500, 0.500], MQ=34.51, POSITIVE_TRAIN_SITE=true, QD=32.87, SOR=0.968, VQSLOD=-7.669e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,24,0:24:75:1|1:908920_C_G:1104,75,0,1104,75,1104	./.:33,0,0:33:.:.:.:0,0,0,0,0,0	2/2:0,0,15:15:45:1|1:908920_C_G:627,627,627,45,45,0 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.446 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.446 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:51.446 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:31:51.446 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:31:51.446 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199004 Q1368.97 of type=SNP alleles=[A*, *, G] attr={AC=[2, 1], AF=[0.500, 0.250], AN=4, DB=true, DP=67, ExcessHet=3.0103, FS=0.000, MLEAC=[2, 1], MLEAF=[0.500, 0.250], MQ=32.71, QD=28.53, SOR=0.302, VQSLOD=-9.124e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,18,0:18:54:1|1:908920_C_G:810,54,0,810,54,810	./.:29,0,0:29:.:.:.:0,0,0,0,0,0	0/2:1,0,15:16:59:0|1:908920_C_G:579,582,687,0,105,59 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.447 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.447 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:51.447 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:31:51.447 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:31:51.447 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199005 Q1434.91 of type=SNP alleles=[A*, *, G] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=0.533, ClippingRankSum=1.60, DB=true, DP=88, ExcessHet=3.9794, FS=0.000, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=49.95, MQRankSum=1.07, NEGATIVE_TRAIN_SITE=true, QD=27.59, ReadPosRankSum=2.40, SOR=0.902, VQSLOD=-9.887e-01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:5,9,0:14:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:264,0,168,283,195,478	0/1:7,8,0:15:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:206,0,264,233,288,521	2/2:0,0,23:23:71:.:.:990,990,990,71,71,0 filters=
14:31:51.447 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
14:31:51.448 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = C, ref T != C reference coding seq) @[chr3:179199006]!  Substituting given allele for sequence code (CTT->TTT)
14:31:51.448 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:31:51.448 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:51.448 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:31:51.448 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:31:51.448 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199006 Q2248.91 of type=SNP alleles=[T*, *, C] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=-9.740e-01, ClippingRankSum=0.545, DB=true, DP=101, ExcessHet=3.9794, FS=6.882, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=49.59, MQRankSum=-1.490e-01, NEGATIVE_TRAIN_SITE=true, QD=23.18, ReadPosRankSum=0.578, SOR=1.028, VQSLOD=-8.789e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:18,17,0:35:99:456,0,705,510,756,1266	0/1:15,17,0:32:99:467,0,579,512,630,1142	2/2:0,0,30:30:91:1351,1351,1351,91,91,0 filters=
14:31:51.448 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
14:31:51.449 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != T reference coding seq) @[chr3:179199007]!  Substituting given allele for sequence code (CTT->CAT)
14:31:51.449 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.449 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:51.449 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:31:51.449 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:31:51.449 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199007 Q1821.97 of type=SNP alleles=[A*, *, G] attr={AC=[2, 1], AF=[0.500, 0.250], AN=4, DB=true, DP=92, ExcessHet=3.0103, FS=10.616, MLEAC=[2, 1], MLEAF=[0.500, 0.250], MQ=32.68, POSITIVE_TRAIN_SITE=true, QD=27.61, SOR=1.479, VQSLOD=-1.050e+01, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	./.:21,0,0:21:.:.:.:0,0,0,0,0,0	1/1:0,31,0:31:96:1|1:996335_C_A:1103,96,0,1103,96,1103	0/2:11,0,24:35:99:.:.:739,773,1159,0,386,316 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.450 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:31:51.450 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:31:51.450 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:31:51.450 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:31:51.450 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199008 Q601.66 of type=SNP alleles=[T*, *, C] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=-5.100e-01, ClippingRankSum=1.36, DB=true, DP=95, ExcessHet=3.9794, FS=27.935, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=48.12, MQRankSum=1.08, NEGATIVE_TRAIN_SITE=true, QD=12.53, ReadPosRankSum=0.849, SOR=2.062, VQSLOD=-3.093e+00, culprit=FS} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:11,7,0:18:88:0|1:1611567_CT_C:88,0,187,121,208,329	2/2:1,0,12:13:16:.:.:212,216,235,16,35,0	0/1:4,13,0:17:20:0|1:1611567_CT_C:327,0,20,339,58,397 filters=VQSRTrancheSNP99.90to100.00+
14:31:51.450 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
14:31:51.451 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: +, alt = G, ref A != C reference coding seq) @[chr3:179199009]!  Substituting given allele for sequence code (CTT->ATT)
14:31:51.451 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:31:51.451 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:31:51.451 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:31:51.451 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:31:51.451 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199009 Q469.89 of type=SNP alleles=[A*, *, G] attr={AC=[2, 2], AF=[0.333, 0.333], AN=6, BaseQRankSum=2.60, ClippingRankSum=1.32, DB=true, DP=80, ExcessHet=3.9794, FS=2.173, MLEAC=[2, 2], MLEAF=[0.333, 0.333], MQ=53.43, MQRankSum=1.82, NEGATIVE_TRAIN_SITE=true, QD=6.44, ReadPosRankSum=1.70, SOR=1.002, VQSLOD=-6.972e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:33,7,0:40:84:84,0,865,180,886,1065	2/2:0,0,9:9:27:332,332,332,27,27,0	0/1:18,6,0:24:79:79,0,466,133,483,616 filters=
14:31:51.451 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
14:31:51.452 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:31:51.452 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:31:51.452 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.640 INFO  Funcotator - ------------------------------------------------------------
14:31:51.640 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.640 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.640 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.640 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.640 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.640 INFO  Funcotator - ------------------------------------------------------------
14:31:51.640 INFO  Funcotator - ------------------------------------------------------------
14:31:51.640 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.640 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.640 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.640 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.640 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.640 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.640 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.640 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.640 INFO  Funcotator - Inflater: IntelInflater
14:31:51.640 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.640 INFO  Funcotator - Requester pays: disabled
14:31:51.640 INFO  Funcotator - Initializing engine
14:31:51.642 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
14:31:51.643 INFO  Funcotator - Done initializing engine
14:31:51.643 INFO  Funcotator - Validating sequence dictionaries...
14:31:51.644 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:51.736 INFO  Funcotator - ------------------------------------------------------------
14:31:51.736 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:51.736 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:51.736 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:51.736 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:51.736 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:51 PM GMT
14:31:51.736 INFO  Funcotator - ------------------------------------------------------------
14:31:51.736 INFO  Funcotator - ------------------------------------------------------------
14:31:51.736 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:51.736 INFO  Funcotator - Picard Version: 3.4.0
14:31:51.736 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:51.736 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:51.736 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:51.736 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:51.736 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:51.736 INFO  Funcotator - Deflater: IntelDeflater
14:31:51.736 INFO  Funcotator - Inflater: IntelInflater
14:31:51.736 INFO  Funcotator - GCS max retries/reopens: 20
14:31:51.736 INFO  Funcotator - Requester pays: disabled
14:31:51.736 INFO  Funcotator - Initializing engine
14:31:51.738 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:31:51.739 INFO  Funcotator - Done initializing engine
14:31:51.739 INFO  Funcotator - Validating sequence dictionaries...
14:31:51.739 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:51.739 INFO  Funcotator - Initializing data sources...
14:31:51.739 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:51.739 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:51.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:51.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:51.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:51.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:51.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:51.741 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:51.742 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:51.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:51.762 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:51.763 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:51.808 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:51.808 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:52.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:52.397 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:52.398 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:52.400 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:52.403 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:52.405 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:52.405 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:52.406 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:52.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:52.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:52.435 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:52.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:52.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:52.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:52.481 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:52.482 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:52.482 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:52.483 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:52.483 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:52.565 INFO  Funcotator - Initializing Funcotator Engine...
14:31:52.565 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:52.565 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:52.565 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator3881380548802665101.vcf
14:31:52.567 INFO  ProgressMeter - Starting traversal
14:31:52.567 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:54.548 INFO  ProgressMeter -             unmapped              0.0                   198           5997.0
14:31:54.548 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:54.548 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:54.557 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3244294144
14:31:54.647 INFO  Funcotator - ------------------------------------------------------------
14:31:54.647 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:54.647 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:54.647 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:54.647 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:54.647 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:54 PM GMT
14:31:54.647 INFO  Funcotator - ------------------------------------------------------------
14:31:54.647 INFO  Funcotator - ------------------------------------------------------------
14:31:54.647 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:54.647 INFO  Funcotator - Picard Version: 3.4.0
14:31:54.647 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:54.647 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:54.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:54.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:54.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:54.647 INFO  Funcotator - Deflater: IntelDeflater
14:31:54.647 INFO  Funcotator - Inflater: IntelInflater
14:31:54.647 INFO  Funcotator - GCS max retries/reopens: 20
14:31:54.647 INFO  Funcotator - Requester pays: disabled
14:31:54.647 INFO  Funcotator - Initializing engine
14:31:54.649 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:31:54.650 INFO  Funcotator - Done initializing engine
14:31:54.650 INFO  Funcotator - Validating sequence dictionaries...
14:31:54.650 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:54.650 INFO  Funcotator - Initializing data sources...
14:31:54.650 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:54.650 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:54.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:54.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:54.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:54.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:54.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:54.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:54.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:54.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:54.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:54.653 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:54.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:54.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:54.672 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:54.672 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:54.717 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:54.717 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:55.305 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:55.305 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:55.306 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:55.308 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:55.311 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:55.313 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:31:55.313 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:55.314 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:31:55.341 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:55.341 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:31:55	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:31:55.341 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:55.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:55.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:55.381 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:55.388 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:55.389 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:55.389 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:55.390 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:55.390 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:55.474 INFO  Funcotator - Initializing Funcotator Engine...
14:31:55.475 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:31:55.475 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:55.475 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator4778810450169991847.maf
14:31:55.475 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:55.475 INFO  ProgressMeter - Starting traversal
14:31:55.476 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:57.459 INFO  ProgressMeter -             unmapped              0.0                   198           5990.9
14:31:57.459 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:31:57.459 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:31:57.459 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3244294144
14:31:57.551 INFO  Funcotator - ------------------------------------------------------------
14:31:57.551 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:57.551 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:57.551 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:57.551 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:57.551 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:57 PM GMT
14:31:57.551 INFO  Funcotator - ------------------------------------------------------------
14:31:57.551 INFO  Funcotator - ------------------------------------------------------------
14:31:57.551 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:57.551 INFO  Funcotator - Picard Version: 3.4.0
14:31:57.551 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:57.551 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:57.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:57.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:57.551 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:57.551 INFO  Funcotator - Deflater: IntelDeflater
14:31:57.551 INFO  Funcotator - Inflater: IntelInflater
14:31:57.551 INFO  Funcotator - GCS max retries/reopens: 20
14:31:57.551 INFO  Funcotator - Requester pays: disabled
14:31:57.551 INFO  Funcotator - Initializing engine
14:31:57.580 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
14:31:57.600 INFO  Funcotator - Done initializing engine
14:31:57.600 INFO  Funcotator - Validating sequence dictionaries...
14:31:57.607 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:57.607 INFO  Funcotator - Initializing data sources...
14:31:57.607 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:57.607 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:57.607 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:57.607 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:57.607 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:57.607 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:57.607 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:57.608 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:57.608 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
14:31:57.609 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
14:31:57.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:57.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
14:31:57.671 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
14:31:57.672 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v90_38.hg38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
14:31:58.281 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:58.281 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:31:58.282 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:58.284 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:58.285 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:31:58.287 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v90_38.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
14:31:58.352 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
14:31:58.352 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
14:31:58.353 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
14:31:58.360 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:58.360 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.361 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:31:58.361 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
14:31:58.362 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.365 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:31:58.365 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator1030103930947595590.vcf
14:31:58.366 INFO  ProgressMeter - Starting traversal
14:31:58.367 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.371 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:31:58.374 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3244294144
14:31:58.463 INFO  Funcotator - ------------------------------------------------------------
14:31:58.463 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:58.463 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:58.463 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:58.463 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:58.463 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:58 PM GMT
14:31:58.463 INFO  Funcotator - ------------------------------------------------------------
14:31:58.463 INFO  Funcotator - ------------------------------------------------------------
14:31:58.463 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:58.463 INFO  Funcotator - Picard Version: 3.4.0
14:31:58.463 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:58.463 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:58.463 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:58.464 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:58.464 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:58.464 INFO  Funcotator - Deflater: IntelDeflater
14:31:58.464 INFO  Funcotator - Inflater: IntelInflater
14:31:58.464 INFO  Funcotator - GCS max retries/reopens: 20
14:31:58.464 INFO  Funcotator - Requester pays: disabled
14:31:58.464 INFO  Funcotator - Initializing engine
14:31:58.466 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
14:31:58.466 INFO  Funcotator - Done initializing engine
14:31:58.466 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:58.466 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:58.466 INFO  Funcotator - Initializing data sources...
14:31:58.466 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
14:31:58.466 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:58.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.repro.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:31:58.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.467 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:58.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.repro.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:31:58.467 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:31:58.468 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:31:58.468 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.repro.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:31:58.469 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:31:58.469 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.469 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.469 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.470 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.471 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.471 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:58.471 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:58.471 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:58.471 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing8706245538262837821.vcf
14:31:58.471 INFO  ProgressMeter - Starting traversal
14:31:58.471 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.476 INFO  ProgressMeter -             unmapped              0.0                     1          12000.0
14:31:58.476 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:31:58.476 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
14:31:58.478 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:58.479 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing8706245538262837821.vcf
14:31:58.569 INFO  Funcotator - ------------------------------------------------------------
14:31:58.569 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:58.569 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:58.569 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:58.569 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:58.569 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:58 PM GMT
14:31:58.569 INFO  Funcotator - ------------------------------------------------------------
14:31:58.569 INFO  Funcotator - ------------------------------------------------------------
14:31:58.569 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:58.569 INFO  Funcotator - Picard Version: 3.4.0
14:31:58.569 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:58.569 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:58.569 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:58.569 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:58.569 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:58.569 INFO  Funcotator - Deflater: IntelDeflater
14:31:58.569 INFO  Funcotator - Inflater: IntelInflater
14:31:58.569 INFO  Funcotator - GCS max retries/reopens: 20
14:31:58.569 INFO  Funcotator - Requester pays: disabled
14:31:58.569 INFO  Funcotator - Initializing engine
14:31:58.570 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:31:58.571 INFO  Funcotator - Done initializing engine
14:31:58.571 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:58.571 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:58.571 INFO  Funcotator - Initializing data sources...
14:31:58.571 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:58.571 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:58.571 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.571 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.571 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.571 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:58.571 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.571 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.572 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.572 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.573 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:58.573 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.575 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.576 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.576 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:58.576 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:58.576 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out4281920976169488801.maf
14:31:58.577 INFO  ProgressMeter - Starting traversal
14:31:58.577 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.579 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178872355 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.823, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178872355, ILLUMINA_STRAND=TOP, N_AA=4, N_AB=194, N_BB=1053, PROBE_A=AATGTGTTACAATCTGTCCCCCACCATATACATATACAAAGTAGCAGTCC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.02, devTHETA_AB=0.035, devTHETA_BB=0.018, devX_AA=0.095, devX_AB=0.05, devX_BB=0.02, devY_AA=0.022, devY_AB=0.06, devY_BB=0.094, meanR_AA=0.748, meanR_AB=0.789, meanR_BB=0.755, meanTHETA_AA=0.052, meanTHETA_AB=0.569, meanTHETA_BB=0.946, meanX_AA=0.692, meanX_AB=0.352, meanX_BB=0.059, meanY_AA=0.056, meanY_AB=0.437, meanY_BB=0.695, refSNP=rs11706842, zthresh_X=0.18402316111, zthresh_Y=0.185250013887} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.514, GTA=1/0, GTZ=1/0, IGC=0.849, LRR=-0.05, NORMX=0.333, NORMY=0.428, R=0.761, THETA=0.579, X=4554, Y=2131}]] filters=
14:31:58.580 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178902506 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=928, GC_SCORE=0.893, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178902506, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=28, N_BB=1220, PROBE_A=TTATTGGACCAGCCTAGACTGAAAATCTTCTGTTTAGGCATTTTGGTGGG, PROBE_B=., SOURCE=psych, devR_AA=0.1, devR_AB=0.105, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.023, devTHETA_BB=0.01, devX_AA=0.101, devX_AB=0.054, devX_BB=0.015, devY_AA=0.031, devY_AB=0.055, devY_BB=0.097, meanR_AA=0.948, meanR_AB=1.181, meanR_BB=0.994, meanTHETA_AA=0.026, meanTHETA_AB=0.512, meanTHETA_BB=0.973, meanX_AA=0.911, meanX_AB=0.58, meanX_BB=0.041, meanY_AA=0.037, meanY_AB=0.602, meanY_BB=0.953, refSNP=rs111868222, zthresh_X=0.140378981558, zthresh_Y=0.166929562077} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.99, GTA=0/0, GTZ=0/0, IGC=0.882, LRR=0.069, NORMX=0.057, NORMY=0.99, R=1.047, THETA=0.963, X=1498, Y=5593}]] filters=
14:31:58.580 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178907849 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.797, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178907849, ILLUMINA_STRAND=TOP, N_AA=19, N_AB=360, N_BB=872, PROBE_A=GAGGCCCTAACTGGGGCCCAGAAAATTGTACTGAAGGATACTTGCTTCCT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.023, devTHETA_AB=0.038, devTHETA_BB=0.021, devX_AA=0.094, devX_AB=0.05, devX_BB=0.018, devY_AA=0.019, devY_AB=0.056, devY_BB=0.093, meanR_AA=0.556, meanR_AB=0.58, meanR_BB=0.576, meanTHETA_AA=0.054, meanTHETA_AB=0.544, meanTHETA_BB=0.94, meanX_AA=0.513, meanX_AB=0.27, meanX_BB=0.05, meanY_AA=0.043, meanY_AB=0.31, meanY_BB=0.526, refSNP=rs9866361, zthresh_X=0.161949964118, zthresh_Y=0.175918019742} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.978, GTA=0/0, GTZ=0/0, IGC=0.811, LRR=-0.054, NORMX=0.061, NORMY=0.495, R=0.555, THETA=0.922, X=1038, Y=2429}]] filters=
14:31:58.581 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916753 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.886, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916753, ILLUMINA_STRAND=TOP, N_AA=1247, N_AB=0, N_BB=0, PROBE_A=GATAGTGACTTTAGAATGCCTCCGTGAGGCTACATTAATAACCATAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.094, devX_AB=0.05, devX_BB=0.017, devY_AA=0.015, devY_AB=0.052, devY_BB=0.098, meanR_AA=0.455, meanR_AB=0.541, meanR_BB=0.503, meanTHETA_AA=0.047, meanTHETA_AB=0.511, meanTHETA_BB=0.976, meanX_AA=0.424, meanX_AB=0.266, meanX_BB=0.018, meanY_AA=0.031, meanY_AB=0.275, meanY_BB=0.485, refSNP=rs190372148, zthresh_X=0.182850738152, zthresh_Y=0.12847847542} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.489, LRR=0.114, NORMX=0.459, NORMY=0.034, R=0.493, THETA=0.047, X=8065, Y=228}]] filters=
14:31:58.581 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916791 Q. of type=SNP alleles=[C*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.89, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916791, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TAACCATAAAGCATGAACTATTTAAAGAAGCAAGAAAATACCCCCTCCAT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.013, devX_AA=0.099, devX_AB=0.053, devX_BB=0.014, devY_AA=0.024, devY_AB=0.052, devY_BB=0.096, meanR_AA=0.738, meanR_AB=0.886, meanR_BB=0.745, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.965, meanX_AA=0.711, meanX_AB=0.447, meanX_BB=0.039, meanY_AA=0.027, meanY_AB=0.439, meanY_BB=0.706, refSNP=rs71310379, zthresh_X=0.133750336661, zthresh_Y=0.164321280546} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.494, LRR=0.001, NORMX=0.022, NORMY=0.718, R=0.741, THETA=0.98, X=620, Y=4057}]] filters=
14:31:58.581 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178921158 Q. of type=SNP alleles=[G*, A] attr={AC=1, AF=0.500, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.788, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178921158, ILLUMINA_STRAND=TOP, N_AA=30, N_AB=414, N_BB=807, PROBE_A=CTTTCGTGCAATTTATATTCAGAAGTGTTTGATTGATCTTGTGCTTCAAC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.016, devTHETA_AB=0.029, devTHETA_BB=0.015, devX_AA=0.094, devX_AB=0.049, devX_BB=0.021, devY_AA=0.019, devY_AB=0.061, devY_BB=0.092, meanR_AA=0.827, meanR_AB=0.983, meanR_BB=0.947, meanTHETA_AA=0.05, meanTHETA_AB=0.585, meanTHETA_BB=0.933, meanX_AA=0.767, meanX_AB=0.426, meanX_BB=0.09, meanY_AA=0.06, meanY_AB=0.557, meanY_BB=0.857, refSNP=rs7623154, zthresh_X=0.224662521322, zthresh_Y=0.204527740428} GT=[[0816201804HC0_R01C01 G*/A {BAF=0.484, GTA=1/0, GTZ=1/0, IGC=0.797, LRR=0.017, NORMX=0.442, NORMY=0.547, R=0.99, THETA=0.567, X=6004, Y=2730}]] filters=
14:31:58.582 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 Q. of type=SNP alleles=[C*, G] attr={AC=0, AF=0.00, ALLELE_A=G, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178922361, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1249, PROBE_A=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACG, PROBE_B=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACC, SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.014, devX_AA=0.099, devX_AB=0.052, devX_BB=0.014, devY_AA=0.022, devY_AB=0.052, devY_BB=0.097, meanR_AA=0.664, meanR_AB=0.793, meanR_BB=0.678, meanTHETA_AA=0.024, meanTHETA_AB=0.501, meanTHETA_BB=0.977, meanX_AA=0.64, meanX_AB=0.396, meanX_BB=0.024, meanY_AA=0.025, meanY_AB=0.397, meanY_BB=0.654, refSNP=rs113613074, zthresh_X=0.119568794798, zthresh_Y=0.156845592246} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.515, LRR=-0.048, NORMX=0.015, NORMY=0.639, R=0.654, THETA=0.986, X=603, Y=11188}]] filters=
14:31:58.582 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=1161, GC_SCORE=0.868, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178927410, ILLUMINA_STRAND=BOT, N_AA=1072, N_AB=169, N_BB=0, PROBE_A=GAGCAAATGGAAAGGCAAAGTCGAGCAGCACGAGGAAGATCAGGAATGTA, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.042, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.058, devX_BB=0.024, devY_AA=0.015, devY_AB=0.059, devY_BB=0.099, meanR_AA=0.829, meanR_AB=0.918, meanR_BB=0.742, meanTHETA_AA=0.017, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=0.808, meanX_AB=0.452, meanX_BB=0.028, meanY_AA=0.021, meanY_AB=0.466, meanY_BB=0.714, refSNP=rs2230461, zthresh_X=0.183044318831, zthresh_Y=0.127662818665} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.009, GTA=0/0, GTZ=0/0, IGC=0.851, LRR=0.267, NORMX=0.961, NORMY=0.038, R=1, THETA=0.025, X=15373, Y=361}]] filters=
14:31:58.583 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=971, GC_SCORE=0.869, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178932551, ILLUMINA_STRAND=TOP, N_AA=343, N_AB=398, N_BB=479, PROBE_A=GTGAAGACCTGCTGTTTTCTCTGCTTCCAAGCTCAACTAACAATATATTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.131, devR_AB=0.1, devR_BB=0.123, devTHETA_AA=0.017, devTHETA_AB=0.023, devTHETA_BB=0.022, devX_AA=0.126, devX_AB=0.061, devX_BB=0.024, devY_AA=0.017, devY_AB=0.074, devY_BB=0.118, meanR_AA=0.622, meanR_AB=0.938, meanR_BB=0.739, meanTHETA_AA=0.028, meanTHETA_AB=0.563, meanTHETA_BB=0.965, meanX_AA=0.596, meanX_AB=0.423, meanX_BB=0.038, meanY_AA=0.026, meanY_AB=0.515, meanY_BB=0.701, refSNP=rs12494623, zthresh_X=0.152176899827, zthresh_Y=0.170103096568} GT=[[0816201804HC0_R01C01 T/T {BAF=0.027, GTA=1/1, GTZ=1/1, IGC=0.906, LRR=-0.336, NORMX=0.465, NORMY=0.042, R=0.507, THETA=0.057, X=7174, Y=362}]] filters=
14:31:58.583 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.891, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178937400, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CATACACAGATGTATTGCTTGGTAAAAGATTGGCCTCCAATCAAACCTGA, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.108, devR_BB=0.1, devTHETA_AA=0.013, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.053, devX_BB=0.026, devY_AA=0.015, devY_AB=0.053, devY_BB=0.1, meanR_AA=0.79, meanR_AB=0.96, meanR_BB=0.803, meanTHETA_AA=0.031, meanTHETA_AB=0.503, meanTHETA_BB=0.976, meanX_AA=0.753, meanX_AB=0.477, meanX_BB=0.029, meanY_AA=0.037, meanY_AB=0.482, meanY_BB=0.773, refSNP=rs137902538, zthresh_X=0.187164813479, zthresh_Y=0.140282002247} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.496, LRR=-0.05, NORMX=0.731, NORMY=0.031, R=0.761, THETA=0.027, X=12748, Y=231}]] filters=
14:31:58.583 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.902, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178947118, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=ACCTTTCAAGCCGCCTTTGCACTGAATTTGCATAATAGTGTGAGAATTTC, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.098, devX_AB=0.052, devX_BB=0.014, devY_AA=0.019, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.576, meanR_AB=0.681, meanR_BB=0.596, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.964, meanX_AA=0.555, meanX_AB=0.344, meanX_BB=0.032, meanY_AA=0.021, meanY_AB=0.337, meanY_BB=0.565, zthresh_X=0.122228724787, zthresh_Y=0.159007429626} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.509, LRR=0.03, NORMX=0.022, NORMY=0.585, R=0.607, THETA=0.977, X=711, Y=3117}]] filters=
14:31:58.584 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.848, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178950297, ILLUMINA_STRAND=BOT, N_AA=486, N_AB=560, N_BB=205, PROBE_A=GTCTGTGTGTCTGCTTTTGTGTGTATCTGCTGTTTTGGTAATTATAGTTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.102, devR_AB=0.12, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.028, devTHETA_BB=0.016, devX_AA=0.099, devX_AB=0.057, devX_BB=0.022, devY_AA=0.018, devY_AB=0.057, devY_BB=0.094, meanR_AA=1.064, meanR_AB=1.186, meanR_BB=1.006, meanTHETA_AA=0.03, meanTHETA_AB=0.494, meanTHETA_BB=0.943, meanX_AA=1.016, meanX_AB=0.598, meanX_BB=0.083, meanY_AA=0.048, meanY_AB=0.587, meanY_BB=0.923, refSNP=rs1607237, zthresh_X=0.199217026256, zthresh_Y=0.172626912202} GT=[[0816201804HC0_R01C01 T/T {BAF=0, GTA=1/1, GTZ=1/1, IGC=0.882, LRR=-0.014, NORMX=1.013, NORMY=0.039, R=1.052, THETA=0.025, X=13288, Y=291}]] filters=
14:31:58.584 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.832, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960744, ILLUMINA_STRAND=BOT, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=AAGATTTCTCTGCTCTTCCTTTGCTCCTCCTCATAATGCACAGTTTGAAC, PROBE_B=., SOURCE=1000_genomes, devR_AA=0.1, devR_AB=0.195, devR_BB=0.113, devTHETA_AA=0.007, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.059, devX_BB=0.042, devY_AA=0.015, devY_AB=0.058, devY_BB=0.117, meanR_AA=1.388, meanR_AB=1.725, meanR_BB=1.296, meanTHETA_AA=0.014, meanTHETA_AB=0.495, meanTHETA_BB=0.975, meanX_AA=1.358, meanX_AB=0.87, meanX_BB=0.048, meanY_AA=0.029, meanY_AB=0.855, meanY_BB=1.248, refSNP=rs200646413, zthresh_X=0.181538312311, zthresh_Y=0.124907131052} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0.004, GTA=0/0, GTZ=0/0, IGC=0.423, LRR=0.033, NORMX=1.384, NORMY=0.039, R=1.423, THETA=0.018, X=24000, Y=330}]] filters=
14:31:58.584 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.847, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960843, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.18, devR_BB=0.106, devTHETA_AA=0.009, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.057, devX_BB=0.04, devY_AA=0.017, devY_AB=0.058, devY_BB=0.11, meanR_AA=1.287, meanR_AB=1.594, meanR_BB=1.215, meanTHETA_AA=0.034, meanTHETA_AB=0.505, meanTHETA_BB=0.976, meanX_AA=1.221, meanX_AB=0.791, meanX_BB=0.044, meanY_AA=0.066, meanY_AB=0.804, meanY_BB=1.171, refSNP=rs145985409, zthresh_X=0.19811140407, zthresh_Y=0.172079887333} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.01, GTA=0/0, GTZ=0/0, IGC=0.441, LRR=0.077, NORMX=1.276, NORMY=0.087, R=1.363, THETA=0.043, X=22154, Y=590}]] filters=
14:31:58.585 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.901, ILLUMINA_BUILD=37.2, ILLUMINA_CHR=3, ILLUMINA_POS=178962380, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=CGACTGGCTGGACTGTGCCTTCACCTGTGGTGTGCACTGCCACGGTCAGG, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.133, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.009, devX_AA=0.101, devX_AB=0.054, devX_BB=0.013, devY_AA=0.032, devY_AB=0.054, devY_BB=0.097, meanR_AA=0.964, meanR_AB=1.179, meanR_BB=0.948, meanTHETA_AA=0.024, meanTHETA_AB=0.5, meanTHETA_BB=0.976, meanX_AA=0.928, meanX_AB=0.589, meanX_BB=0.034, meanY_AA=0.036, meanY_AB=0.59, meanY_BB=0.915, refSNP=rs199686819, zthresh_X=0.12173904259, zthresh_Y=0.159179424244} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.508, LRR=-0.062, NORMX=0.033, NORMY=0.876, R=0.909, THETA=0.976, X=819, Y=4947}]] filters=
14:31:58.585 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.879, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178962425, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=GAGAGAAGAATCGACCTGCACTGCCATCCACACAGATATCATGGACGACT, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.121, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.011, devX_AA=0.101, devX_AB=0.054, devX_BB=0.014, devY_AA=0.029, devY_AB=0.053, devY_BB=0.095, meanR_AA=0.883, meanR_AB=1.074, meanR_BB=0.877, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.851, meanX_AB=0.543, meanX_BB=0.048, meanY_AA=0.032, meanY_AB=0.532, meanY_BB=0.829, refSNP=rs145138176, zthresh_X=0.14237441016, zthresh_Y=0.168724424863} GT=[[0816201804HC0_R01C01 C*/C* {BAF=0.999, GTA=0/0, GTZ=0/0, IGC=0.48, LRR=-0.121, NORMX=0.045, NORMY=0.761, R=0.806, THETA=0.963, X=1125, Y=4047}]] filters=
14:31:58.586 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968543 Q. of type=SNP alleles=[G*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968543, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=1, N_BB=1250, PROBE_A=GGGCTTCTCAGTCCTAATGTTCTTCTTGCTCGGAACAACCATTCTAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.104, devR_AB=0.156, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.008, devX_AA=0.107, devX_AB=0.058, devX_BB=0.014, devY_AA=0.036, devY_AB=0.057, devY_BB=0.097, meanR_AA=1.1, meanR_AB=1.381, meanR_BB=1.127, meanTHETA_AA=0.025, meanTHETA_AB=0.492, meanTHETA_BB=0.975, meanX_AA=1.059, meanX_AB=0.7, meanX_BB=0.042, meanY_AA=0.041, meanY_AB=0.682, meanY_BB=1.085, refSNP=rs61734056, zthresh_X=0.135160960006, zthresh_Y=0.165299195841} GT=[[0816201804HC0_R01C01 G*/G* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.897, LRR=0.034, NORMX=0.04, NORMY=1.113, R=1.153, THETA=0.977, X=972, Y=6285}]] filters=
14:31:58.586 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968568 Q. of type=SNP alleles=[A*, C] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=C, AN=2, BEADSET_ID=1168, GC_SCORE=0.889, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968568, ILLUMINA_STRAND=BOT, N_AA=1249, N_AB=1, N_BB=0, PROBE_A=CCGTGATGCTGGGGTTTGCCATGATGGGCTTCTCAGTCCTAATGTTCTTC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.143, devR_AB=0.175, devR_BB=0.109, devTHETA_AA=0.01, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.14, devX_AB=0.076, devX_BB=0.041, devY_AA=0.016, devY_AB=0.077, devY_BB=0.113, meanR_AA=1.113, meanR_AB=1.547, meanR_BB=1.25, meanTHETA_AA=0.019, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=1.081, meanX_AB=0.763, meanX_BB=0.046, meanY_AA=0.032, meanY_AB=0.784, meanY_BB=1.204, refSNP=rs2276802, zthresh_X=0.189602852188, zthresh_Y=0.145988814983} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.878, LRR=-0.023, NORMX=1.069, NORMY=0.021, R=1.089, THETA=0.012, X=17958, Y=362}]] filters=
14:31:58.587 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968634 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.885, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968634, ILLUMINA_STRAND=TOP, N_AA=216, N_AB=596, N_BB=439, PROBE_A=ACTACAGTGATGGAGACCCACTAGATGTGCACAAGAGGCTGCCATCCAGT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.011, devTHETA_AB=0.025, devTHETA_BB=0.01, devX_AA=0.096, devX_AB=0.058, devX_BB=0.015, devY_AA=0.019, devY_AB=0.054, devY_BB=0.097, meanR_AA=1.156, meanR_AB=1.266, meanR_BB=0.992, meanTHETA_AA=0.036, meanTHETA_AB=0.47, meanTHETA_BB=0.972, meanX_AA=1.094, meanX_AB=0.662, meanX_BB=0.042, meanY_AA=0.062, meanY_AB=0.603, meanY_BB=0.951, refSNP=rs7645550, zthresh_X=0.139062088415, zthresh_Y=0.166539592425} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.496, GTA=1/0, GTZ=1/0, IGC=0.922, LRR=-0.041, NORMX=0.647, NORMY=0.582, R=1.23, THETA=0.466, X=11372, Y=3338}]] filters=
14:31:58.587 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968660 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.862, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968660, ILLUMINA_STRAND=TOP, N_AA=987, N_AB=246, N_BB=18, PROBE_A=TGCCTCAGGGAAGAAGAGAGAGACAGACTACAGTGATGGAGACCCACTAG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.01, devTHETA_AB=0.039, devTHETA_BB=0.016, devX_AA=0.096, devX_AB=0.061, devX_BB=0.022, devY_AA=0.015, devY_AB=0.061, devY_BB=0.098, meanR_AA=1.016, meanR_AB=1.151, meanR_BB=0.92, meanTHETA_AA=0.036, meanTHETA_AB=0.5, meanTHETA_BB=0.97, meanX_AA=0.962, meanX_AB=0.575, meanX_BB=0.041, meanY_AA=0.054, meanY_AB=0.576, meanY_BB=0.878, refSNP=rs1170672, zthresh_X=0.191295862566, zthresh_Y=0.153061435119} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.899, LRR=0.047, NORMX=1.001, NORMY=0.046, R=1.048, THETA=0.029, X=17415, Y=341}]] filters=
14:31:58.588 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968848 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.884, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968848, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TATTTAGATGGACTTTTCACCAAGCTCTGAACTGGGATTTCATTTTGTTG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.099, devX_AB=0.052, devX_BB=0.015, devY_AA=0.022, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.662, meanR_AB=0.79, meanR_BB=0.676, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.638, meanX_AB=0.399, meanX_BB=0.037, meanY_AA=0.024, meanY_AB=0.391, meanY_BB=0.639, refSNP=rs113011029, zthresh_X=0.138051204865, zthresh_Y=0.165472197716} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.988, GTA=0/0, GTZ=0/0, IGC=0.486, LRR=0.095, NORMX=0.051, NORMY=0.674, R=0.725, THETA=0.952, X=1106, Y=3811}]] filters=
14:31:58.588 INFO  ProgressMeter -             unmapped              0.0                    21         114545.5
14:31:58.588 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:31:58.588 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:31:58.588 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:58.592 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:58.594 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:31:58.687 INFO  Funcotator - ------------------------------------------------------------
14:31:58.687 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:58.687 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:58.687 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:58.687 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:58.687 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:58 PM GMT
14:31:58.687 INFO  Funcotator - ------------------------------------------------------------
14:31:58.687 INFO  Funcotator - ------------------------------------------------------------
14:31:58.687 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:58.688 INFO  Funcotator - Picard Version: 3.4.0
14:31:58.688 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:58.688 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:58.688 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:58.688 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:58.688 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:58.688 INFO  Funcotator - Deflater: IntelDeflater
14:31:58.688 INFO  Funcotator - Inflater: IntelInflater
14:31:58.688 INFO  Funcotator - GCS max retries/reopens: 20
14:31:58.688 INFO  Funcotator - Requester pays: disabled
14:31:58.688 INFO  Funcotator - Initializing engine
14:31:58.688 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:31:58.690 INFO  Funcotator - Done initializing engine
14:31:58.690 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:58.690 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:58.690 INFO  Funcotator - Initializing data sources...
14:31:58.690 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:58.690 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:58.690 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.690 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.690 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.690 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:58.690 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.690 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.691 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.691 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.691 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.691 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:58.692 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.693 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.694 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.694 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.694 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:58.694 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:58.695 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7206697252992236881.vcf
14:31:58.698 INFO  ProgressMeter - Starting traversal
14:31:58.698 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.706 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
14:31:58.706 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:31:58.706 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:31:58.730 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:58.731 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7206697252992236881.vcf
14:31:58.818 INFO  Funcotator - ------------------------------------------------------------
14:31:58.818 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:58.818 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:58.818 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:58.818 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:58.818 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:58 PM GMT
14:31:58.818 INFO  Funcotator - ------------------------------------------------------------
14:31:58.818 INFO  Funcotator - ------------------------------------------------------------
14:31:58.818 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:58.818 INFO  Funcotator - Picard Version: 3.4.0
14:31:58.818 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:58.818 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:58.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:58.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:58.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:58.818 INFO  Funcotator - Deflater: IntelDeflater
14:31:58.818 INFO  Funcotator - Inflater: IntelInflater
14:31:58.818 INFO  Funcotator - GCS max retries/reopens: 20
14:31:58.818 INFO  Funcotator - Requester pays: disabled
14:31:58.818 INFO  Funcotator - Initializing engine
14:31:58.820 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_3_miss_clinvar_alt_only.vcf
14:31:58.820 INFO  Funcotator - Done initializing engine
14:31:58.820 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:58.820 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:58.820 INFO  Funcotator - Initializing data sources...
14:31:58.820 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:58.820 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:58.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.821 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:58.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.821 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.821 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.822 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:58.822 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.823 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.824 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.825 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.825 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:58.825 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.
14:31:58.825 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:58.825 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14981581069486173087.vcf
14:31:58.826 INFO  ProgressMeter - Starting traversal
14:31:58.826 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.830 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
14:31:58.830 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:31:58.830 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:31:58.832 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:58.833 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14981581069486173087.vcf
14:31:58.923 INFO  Funcotator - ------------------------------------------------------------
14:31:58.923 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:58.923 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:58.923 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:58.923 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:58.923 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:58 PM GMT
14:31:58.923 INFO  Funcotator - ------------------------------------------------------------
14:31:58.923 INFO  Funcotator - ------------------------------------------------------------
14:31:58.923 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:58.923 INFO  Funcotator - Picard Version: 3.4.0
14:31:58.923 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:58.923 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:58.923 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:58.923 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:58.923 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:58.923 INFO  Funcotator - Deflater: IntelDeflater
14:31:58.923 INFO  Funcotator - Inflater: IntelInflater
14:31:58.923 INFO  Funcotator - GCS max retries/reopens: 20
14:31:58.923 INFO  Funcotator - Requester pays: disabled
14:31:58.923 INFO  Funcotator - Initializing engine
14:31:58.924 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
14:31:58.924 INFO  Funcotator - Done initializing engine
14:31:58.924 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:58.924 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:58.924 INFO  Funcotator - Initializing data sources...
14:31:58.924 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:58.924 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:58.925 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.925 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.925 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.925 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:58.925 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.925 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:58.926 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:58.926 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:58.926 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.926 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:58.927 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.927 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.928 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:58.929 INFO  Funcotator - Initializing Funcotator Engine...
14:31:58.929 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:58.929 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.
14:31:58.929 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:58.929 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3217478269539795077.vcf
14:31:58.930 INFO  ProgressMeter - Starting traversal
14:31:58.930 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:58.938 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
14:31:58.938 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:31:58.938 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:31:58.940 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:59.032 INFO  Funcotator - ------------------------------------------------------------
14:31:59.032 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:59.032 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.032 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:59.032 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:59.032 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:59 PM GMT
14:31:59.032 INFO  Funcotator - ------------------------------------------------------------
14:31:59.032 INFO  Funcotator - ------------------------------------------------------------
14:31:59.032 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:59.032 INFO  Funcotator - Picard Version: 3.4.0
14:31:59.032 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:59.032 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.032 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.032 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.032 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.032 INFO  Funcotator - Deflater: IntelDeflater
14:31:59.032 INFO  Funcotator - Inflater: IntelInflater
14:31:59.032 INFO  Funcotator - GCS max retries/reopens: 20
14:31:59.032 INFO  Funcotator - Requester pays: disabled
14:31:59.032 INFO  Funcotator - Initializing engine
14:31:59.033 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
14:31:59.034 INFO  Funcotator - Done initializing engine
14:31:59.034 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:59.034 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:59.034 INFO  Funcotator - Initializing data sources...
14:31:59.034 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:59.034 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:59.034 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.034 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.034 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.034 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:59.034 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.035 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:59.035 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.035 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.036 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.036 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:59.037 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.038 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.039 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.040 INFO  Funcotator - Initializing Funcotator Engine...
14:31:59.040 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:59.040 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:59.040 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:59.040 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7925940740287586818.maf
14:31:59.040 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:59.040 INFO  ProgressMeter - Starting traversal
14:31:59.040 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:59.042 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
14:31:59.043 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.044 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.044 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.045 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
14:31:59.045 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
14:31:59.045 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.046 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
14:31:59.046 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.046 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
14:31:59.046 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.047 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
14:31:59.047 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178943785 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:31:59.047 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178947158 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
14:31:59.048 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178952085 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
14:31:59.048 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
14:31:59.048 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:31:59.048 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:31:59.048 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:59.049 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3217478269539795077.vcf
14:31:59.144 INFO  Funcotator - ------------------------------------------------------------
14:31:59.144 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:59.144 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.144 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:59.144 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:59.144 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:59 PM GMT
14:31:59.144 INFO  Funcotator - ------------------------------------------------------------
14:31:59.144 INFO  Funcotator - ------------------------------------------------------------
14:31:59.144 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:59.144 INFO  Funcotator - Picard Version: 3.4.0
14:31:59.144 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:59.144 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.144 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.144 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.144 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.144 INFO  Funcotator - Deflater: IntelDeflater
14:31:59.144 INFO  Funcotator - Inflater: IntelInflater
14:31:59.144 INFO  Funcotator - GCS max retries/reopens: 20
14:31:59.144 INFO  Funcotator - Requester pays: disabled
14:31:59.144 INFO  Funcotator - Initializing engine
14:31:59.146 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:31:59.146 INFO  Funcotator - Done initializing engine
14:31:59.146 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:59.146 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:59.146 INFO  Funcotator - Initializing data sources...
14:31:59.146 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:59.146 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:59.146 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.146 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.147 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:59.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.147 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:59.147 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.148 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.148 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.148 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:59.148 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.149 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.150 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.151 INFO  Funcotator - Initializing Funcotator Engine...
14:31:59.151 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:59.151 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:59.151 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:59.151 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8212528683323511619.vcf
14:31:59.152 INFO  ProgressMeter - Starting traversal
14:31:59.152 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:59.201 INFO  ProgressMeter -             unmapped              0.0                    57          69795.9
14:31:59.201 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:31:59.201 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:59.204 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:59.293 INFO  Funcotator - ------------------------------------------------------------
14:31:59.293 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:59.293 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.293 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:59.293 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:59.293 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:59 PM GMT
14:31:59.293 INFO  Funcotator - ------------------------------------------------------------
14:31:59.293 INFO  Funcotator - ------------------------------------------------------------
14:31:59.294 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:59.294 INFO  Funcotator - Picard Version: 3.4.0
14:31:59.294 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:59.294 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.294 INFO  Funcotator - Deflater: IntelDeflater
14:31:59.294 INFO  Funcotator - Inflater: IntelInflater
14:31:59.294 INFO  Funcotator - GCS max retries/reopens: 20
14:31:59.294 INFO  Funcotator - Requester pays: disabled
14:31:59.294 INFO  Funcotator - Initializing engine
14:31:59.295 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:31:59.295 INFO  Funcotator - Done initializing engine
14:31:59.295 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:59.295 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:59.295 INFO  Funcotator - Initializing data sources...
14:31:59.295 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:31:59.295 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:59.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.296 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:59.296 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.296 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:31:59.296 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:31:59.297 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:31:59.297 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.297 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:31:59.297 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:31:59.301 INFO  Funcotator - Initializing Funcotator Engine...
14:31:59.301 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:31:59.301 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:31:59.301 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:31:59.301 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8453472407606951400.maf
14:31:59.301 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:31:59.301 INFO  ProgressMeter - Starting traversal
14:31:59.301 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:31:59.305 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
14:31:59.306 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
14:31:59.306 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 @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
14:31:59.306 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 @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:31:59.307 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
14:31:59.308 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
14:31:59.308 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:31:59.309 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 @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
14:31:59.309 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 @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:31:59.309 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 @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:31:59.309 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 @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:31:59.310 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 @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:31:59.310 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 @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
14:31:59.311 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 @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
14:31:59.312 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
14:31:59.312 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
14:31:59.313 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 @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
14:31:59.313 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 @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
14:31:59.313 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 @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
14:31:59.313 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 @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
14:31:59.315 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 @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:31:59.315 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
14:31:59.316 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
14:31:59.316 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 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:31:59.317 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
14:31:59.318 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 @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:31:59.318 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
14:31:59.319 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
14:31:59.320 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:31:59.320 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 @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:31:59.320 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:31:59.321 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:31:59.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:31:59.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:31:59.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
14:31:59.323 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
14:31:59.324 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:31:59.325 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
14:31:59.325 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
14:31:59.326 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
14:31:59.326 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
14:31:59.327 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
14:31:59.327 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
14:31:59.328 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
14:31:59.328 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
14:31:59.329 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
14:31:59.329 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
14:31:59.330 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
14:31:59.330 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
14:31:59.331 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
14:31:59.332 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
14:31:59.332 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
14:31:59.332 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
14:31:59.333 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
14:31:59.334 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
14:31:59.334 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
14:31:59.334 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
14:31:59.334 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
14:31:59.334 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:31:59.335 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:31:59.335 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:31:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:31:59.336 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8212528683323511619.vcf
14:31:59.429 INFO  Funcotator - ------------------------------------------------------------
14:31:59.429 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:31:59.429 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.429 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:31:59.429 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:31:59.429 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:31:59 PM GMT
14:31:59.429 INFO  Funcotator - ------------------------------------------------------------
14:31:59.429 INFO  Funcotator - ------------------------------------------------------------
14:31:59.429 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:31:59.429 INFO  Funcotator - Picard Version: 3.4.0
14:31:59.429 INFO  Funcotator - Built for Spark Version: 3.5.0
14:31:59.429 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.429 INFO  Funcotator - Deflater: IntelDeflater
14:31:59.429 INFO  Funcotator - Inflater: IntelInflater
14:31:59.429 INFO  Funcotator - GCS max retries/reopens: 20
14:31:59.429 INFO  Funcotator - Requester pays: disabled
14:31:59.429 INFO  Funcotator - Initializing engine
14:31:59.430 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
14:31:59.431 INFO  Funcotator - Done initializing engine
14:31:59.431 INFO  Funcotator - Skipping sequence dictionary validation.
14:31:59.431 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:31:59.431 INFO  Funcotator - Initializing data sources...
14:31:59.431 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:31:59.431 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:31:59.432 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:31:59.433 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:31:59.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:31:59.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:31:59.434 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:31:59.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:31:59.434 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:31:59.453 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:31:59.454 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:31:59.500 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:31:59.501 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:32:00.156 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:00.156 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:32:00.157 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:00.159 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:00.162 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:00.164 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:32:00.164 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:32:00.165 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:32:00.192 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:32:00.192 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:32:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:32:00.192 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:32:00.231 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:32:00.231 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:32:00.232 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:32:00.239 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:32:00.240 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:32:00.240 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:00.241 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:32:00.241 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:32:00.328 INFO  Funcotator - Initializing Funcotator Engine...
14:32:00.328 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:32:00.328 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:32:00.328 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12738324862796742756.vcf
14:32:00.329 INFO  ProgressMeter - Starting traversal
14:32:00.329 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:16.160 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7580.1
14:32:16.641 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
14:32:16.642 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
14:32:17.413 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7224.3
14:32:17.413 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:32:17.413 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:32:17.415 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=3244294144
14:32:17.516 INFO  Funcotator - ------------------------------------------------------------
14:32:17.516 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:17.516 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:17.516 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:17.516 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:17.516 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:17 PM GMT
14:32:17.516 INFO  Funcotator - ------------------------------------------------------------
14:32:17.516 INFO  Funcotator - ------------------------------------------------------------
14:32:17.517 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:17.517 INFO  Funcotator - Picard Version: 3.4.0
14:32:17.517 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:17.517 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:17.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:17.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:17.517 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:17.517 INFO  Funcotator - Deflater: IntelDeflater
14:32:17.517 INFO  Funcotator - Inflater: IntelInflater
14:32:17.517 INFO  Funcotator - GCS max retries/reopens: 20
14:32:17.517 INFO  Funcotator - Requester pays: disabled
14:32:17.517 INFO  Funcotator - Initializing engine
14:32:17.518 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
14:32:17.518 INFO  Funcotator - Done initializing engine
14:32:17.518 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:17.518 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:17.518 INFO  Funcotator - Initializing data sources...
14:32:17.518 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:32:17.518 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:17.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:32:17.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:32:17.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:32:17.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:32:17.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:32:17.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:32:17.521 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
14:32:17.521 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:32:17.541 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:32:17.541 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
14:32:17.588 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
14:32:17.589 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
14:32:18.176 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:18.176 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:32:18.177 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:18.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:18.182 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:32:18.184 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:32:18.185 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:32:18.185 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:32:18.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
14:32:18.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:32:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:32:18.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
14:32:18.252 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
14:32:18.252 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:32:18.252 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
14:32:18.260 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:32:18.260 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:32:18.260 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:18.261 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:32:18.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
14:32:18.396 INFO  Funcotator - Initializing Funcotator Engine...
14:32:18.396 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:32:18.396 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:32:18.396 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out18282912657073077360.maf
14:32:18.396 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:32:18.397 INFO  ProgressMeter - Starting traversal
14:32:18.397 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:34.083 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7650.1
14:32:34.552 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
14:32:34.554 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = T, ref G != T reference coding seq) @[chr19:8996322]!  Substituting given allele for sequence code (AAT->AAG)
14:32:35.288 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7306.8
14:32:35.288 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:32:35.289 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:32:35.289 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=3244294144
14:32:35.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12738324862796742756.vcf
14:32:35.698 INFO  Funcotator - ------------------------------------------------------------
14:32:35.698 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:35.698 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:35.698 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:35.698 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:35.698 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:35 PM GMT
14:32:35.698 INFO  Funcotator - ------------------------------------------------------------
14:32:35.698 INFO  Funcotator - ------------------------------------------------------------
14:32:35.698 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:35.698 INFO  Funcotator - Picard Version: 3.4.0
14:32:35.698 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:35.698 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:35.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:35.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:35.698 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:35.698 INFO  Funcotator - Deflater: IntelDeflater
14:32:35.698 INFO  Funcotator - Inflater: IntelInflater
14:32:35.698 INFO  Funcotator - GCS max retries/reopens: 20
14:32:35.698 INFO  Funcotator - Requester pays: disabled
14:32:35.698 INFO  Funcotator - Initializing engine
14:32:35.699 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:32:35.716 INFO  Funcotator - Done initializing engine
14:32:35.716 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:35.716 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:35.716 INFO  Funcotator - Initializing data sources...
14:32:35.716 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:32:35.716 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:35.716 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.716 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:32:35.716 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.716 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:35.716 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.716 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:35.717 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.718 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:32:35.718 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.718 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:32:35.719 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.735 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.743 INFO  Funcotator - Initializing Funcotator Engine...
14:32:35.747 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:32:35.747 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10459218168317404333.vcf
14:32:35.760 INFO  ProgressMeter - Starting traversal
14:32:35.760 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:35.783 INFO  ProgressMeter -             unmapped              0.0                   100         260869.6
14:32:35.783 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:32:35.783 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:32:35.789 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:35.877 INFO  Funcotator - ------------------------------------------------------------
14:32:35.877 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:35.877 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:35.877 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:35.877 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:35.877 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:35 PM GMT
14:32:35.877 INFO  Funcotator - ------------------------------------------------------------
14:32:35.877 INFO  Funcotator - ------------------------------------------------------------
14:32:35.877 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:35.877 INFO  Funcotator - Picard Version: 3.4.0
14:32:35.877 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:35.877 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:35.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:35.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:35.877 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:35.877 INFO  Funcotator - Deflater: IntelDeflater
14:32:35.877 INFO  Funcotator - Inflater: IntelInflater
14:32:35.877 INFO  Funcotator - GCS max retries/reopens: 20
14:32:35.877 INFO  Funcotator - Requester pays: disabled
14:32:35.877 INFO  Funcotator - Initializing engine
14:32:35.878 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:32:35.895 INFO  Funcotator - Done initializing engine
14:32:35.895 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:35.895 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:35.895 INFO  Funcotator - Initializing data sources...
14:32:35.895 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:32:35.895 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:35.895 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.895 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:32:35.895 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.895 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:35.895 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.895 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:35.896 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA.gtf
14:32:35.896 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
14:32:35.897 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.897 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:32:35.897 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.914 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
14:32:35.922 INFO  Funcotator - Initializing Funcotator Engine...
14:32:35.926 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:32:35.926 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8693534871198409052.maf
14:32:35.926 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:32:35.926 INFO  ProgressMeter - Starting traversal
14:32:35.926 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:35.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179126640-179126641 Q178.26 of type=INDEL alleles=[AT*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.408, ClippingRankSum=-6.260e-01, DB=true, DP=81, ExcessHet=3.0103, FS=6.956, MLEAC=1, MLEAF=0.167, MQ=59.86, MQRankSum=1.22, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=7.13, ReadPosRankSum=-7.890e-01, SOR=2.424, VQSLOD=0.274, culprit=FS} GT=GT:AD:DP:GQ:PGT:PID:PL	0/0:23,0:23:66:.:.:0,66,769	0/0:24,0:24:23:.:.:0,23,686	0/1:13,12:25:99:0|1:179126640_AT_A:187,0,259 filters=
14:32:35.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179127567 Q312.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.097, ClippingRankSum=0.954, DB=true, DP=93, ExcessHet=3.0103, FS=1.440, MLEAC=1, MLEAF=0.167, MQ=54.41, MQRankSum=-3.289e+00, NEGATIVE_TRAIN_SITE=true, QD=9.76, ReadPosRankSum=0.993, SOR=0.392, VQSLOD=-1.168e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:79:0,79,1018	0/0:30,0:30:90:0,90,982	0/1:20,12:32:99:321,0,579 filters=
14:32:35.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179128974 Q1462.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.580, ClippingRankSum=0.348, DB=true, DP=63, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=38.22, MQRankSum=-2.159e+00, QD=23.22, ReadPosRankSum=-2.300e-02, SOR=0.823, VQSLOD=-5.665e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,17:17:51:581,51,0	1/1:0,18:18:54:600,54,0	0/1:16,12:28:99:296,0,462 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179129966 Q471.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.129e+00, ClippingRankSum=2.07, DB=true, DP=97, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=44.70, MQRankSum=-2.728e+00, QD=16.83, ReadPosRankSum=1.55, SOR=0.871, VQSLOD=-2.880e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:90:0,90,1350	0/0:38,0:38:99:0,114,1181	0/1:11,17:28:99:480,0,297 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179130674 Q425.12 of type=SNP alleles=[A*, G] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-6.110e-01, ClippingRankSum=1.19, DB=true, DP=80, ExcessHet=3.9794, FS=6.065, MLEAC=2, MLEAF=0.333, MQ=40.44, MQRankSum=-5.530e-01, QD=8.02, ReadPosRankSum=1.71, SOR=1.596, VQSLOD=-5.340e+00, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:1|0:179130671_G_T:187,0,590	0/1:16,10:26:99:.:.:249,0,464	0/0:27,0:27:56:.:.:0,56,879 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179134890 Q30.94 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.426, ClippingRankSum=-2.840e-01, DB=true, DP=82, ExcessHet=4.7712, FS=19.638, MLEAC=1, MLEAF=0.167, MQ=59.10, MQRankSum=0.853, NEGATIVE_TRAIN_SITE=true, QD=1.29, ReadPosRankSum=-1.706e+00, SOR=3.590, VQSLOD=-4.392e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:0:0,0,686	0/0:30,0:30:0:0,0,785	0/1:19,5:24:37:37,0,445 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179135392-179135396 Q855.09 of type=INDEL alleles=[CATAT*, C, CAT, CATATAT] attr={AC=[1, 2, 2], AF=[0.167, 0.333, 0.333], AN=6, BaseQRankSum=0.591, ClippingRankSum=-1.970e-01, DB=true, DP=63, ExcessHet=3.0103, FS=0.000, MLEAC=[1, 2, 2], MLEAF=[0.167, 0.333, 0.333], MQ=59.47, MQRankSum=1.38, QD=21.38, ReadPosRankSum=-4.000e-01, SOR=0.770, VQSLOD=2.43, culprit=FS} GT=GT:AD:DP:GQ:PL	1/2:0,2,5,0:7:54:180,146,284,54,0,60,180,146,54,180	2/3:0,0,6,9:15:99:535,535,535,375,375,357,177,177,0,266	0/3:13,0,0,5:18:99:171,210,787,210,787,787,0,577,577,562 filters=
14:32:35.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179139036 Q2999.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-4.360e-01, ClippingRankSum=-1.497e+00, DB=true, DP=119, ExcessHet=3.0103, FS=0.876, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.470e-01, POSITIVE_TRAIN_SITE=true, QD=25.21, ReadPosRankSum=0.931, SOR=0.913, VQSLOD=16.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1077,99,0	1/1:0,42:42:99:1409,126,0	0/1:24,20:44:99:528,0,682 filters=
14:32:35.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179140609 Q69.99 of type=INDEL alleles=[C*, CA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.978, ClippingRankSum=-5.330e-01, DB=true, DP=66, ExcessHet=3.9794, FS=2.480, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.437, NEGATIVE_TRAIN_SITE=true, QD=5.38, ReadPosRankSum=0.533, SOR=1.981, VQSLOD=-1.111e+00, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:21,0:21:0:0,0,39	0/1:8,5:13:76:76,0,120	0/0:26,0:26:0:0,0,506 filters=
14:32:35.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179143781 Q477.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.21, ClippingRankSum=0.343, DB=true, DP=101, ExcessHet=3.0103, FS=8.008, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.886, POSITIVE_TRAIN_SITE=true, QD=14.46, ReadPosRankSum=0.705, SOR=0.511, VQSLOD=16.48, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,101,1267	0/0:31,0:31:90:0,90,1168	0/1:15,18:33:99:486,0,402 filters=
14:32:35.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179145270 Q467.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.60, ClippingRankSum=-1.870e-01, DP=94, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.040e-01, QD=15.58, ReadPosRankSum=0.644, SOR=0.941, VQSLOD=15.70, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,99,1485	0/1:14,16:30:99:476,0,330	0/0:27,0:27:81:0,81,838 filters=
14:32:35.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179145549 Q26.98 of type=INDEL alleles=[C*, CA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.888, ClippingRankSum=0.691, DP=58, ExcessHet=4.7712, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=58.74, MQRankSum=-1.875e+00, NEGATIVE_TRAIN_SITE=true, QD=2.08, ReadPosRankSum=-6.910e-01, SOR=0.260, VQSLOD=-5.419e-01, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:18,0:18:0:0,0,278	0/0:19,0:19:0:0,0,263	0/1:11,2:13:33:33,0,159 filters=
14:32:35.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179150203 Q257.25 of type=SNP alleles=[T*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.427, ClippingRankSum=-7.500e-02, DP=100, ExcessHet=3.0103, FS=1.768, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.276, QD=9.53, ReadPosRankSum=0.025, SOR=1.402, VQSLOD=15.42, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:76:0,76,1186	0/0:36,0:36:99:0,100,1272	0/1:17,10:27:99:266,0,505 filters=
14:32:35.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179153825-179153826 Q3030.89 of type=INDEL alleles=[TG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-4.150e-01, ClippingRankSum=0.327, DB=true, DP=114, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-5.890e-01, POSITIVE_TRAIN_SITE=true, QD=27.31, ReadPosRankSum=-6.330e-01, SOR=0.627, VQSLOD=5.19, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1013,93,0	1/1:0,51:51:99:1662,153,0	0/1:15,14:29:99:370,0,399 filters=
14:32:35.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179162859 Q215.29 of type=INDEL alleles=[T*, TA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.426, ClippingRankSum=0.182, DP=112, ExcessHet=3.0103, FS=1.451, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.872, QD=6.94, ReadPosRankSum=0.791, SOR=0.957, VQSLOD=0.879, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,105,1255	0/0:41,0:41:88:0,88,1285	0/1:19,12:31:99:224,0,411 filters=
14:32:35.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179163705 Q523.25 of type=SNP alleles=[A*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-4.440e-01, ClippingRankSum=-3.200e-02, DB=true, DP=102, ExcessHet=3.0103, FS=6.944, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.317, POSITIVE_TRAIN_SITE=true, QD=14.53, ReadPosRankSum=0.697, SOR=0.750, VQSLOD=17.08, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:90:0,90,1043	0/0:34,0:34:99:0,102,1121	0/1:17,19:36:99:532,0,471 filters=
14:32:35.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170066 Q304.31 of type=INDEL alleles=[A*, ACG] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.317, ClippingRankSum=-1.000e+00, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.635e+00, QD=11.27, ReadPosRankSum=0.903, SOR=0.582, VQSLOD=2.47, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:45:0,45,675	0/0:36,0:36:18:0,18,270	0/1:15,12:27:99:313,0,416 filters=
14:32:35.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170076 Q2160.25 of type=INDEL alleles=[G*, GCA, GCACA] attr={AC=[3, 1], AF=[0.500, 0.167], AN=6, BaseQRankSum=2.14, ClippingRankSum=1.71, DP=97, ExcessHet=3.9794, FS=2.020, MLEAC=[3, 1], MLEAF=[0.500, 0.167], MQ=60.00, MQRankSum=0.066, POSITIVE_TRAIN_SITE=true, QD=27.70, ReadPosRankSum=0.131, SOR=0.633, VQSLOD=3.22, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/1:11,11,0:22:99:429,0,498,462,531,993	1/1:0,28,0:28:93:1368,93,0,1368,93,1369	0/2:14,0,14:28:99:386,399,763,0,365,414 filters=
14:32:35.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179172828 Q461.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.306, ClippingRankSum=-8.830e-01, DB=true, DP=103, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.420e-01, POSITIVE_TRAIN_SITE=true, QD=13.98, ReadPosRankSum=0.342, SOR=0.582, VQSLOD=17.04, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,99,1485	0/0:36,0:36:99:0,102,1211	0/1:16,17:33:99:470,0,437 filters=
14:32:35.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173402 Q170.95 of type=SNP alleles=[T*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-3.260e-01, ClippingRankSum=1.23, DP=85, ExcessHet=4.7712, FS=29.768, MLEAC=1, MLEAF=0.167, MQ=59.76, MQRankSum=0.176, NEGATIVE_TRAIN_SITE=true, QD=6.33, ReadPosRankSum=-2.084e+00, SOR=4.799, VQSLOD=-9.051e+00, culprit=FS} GT=GT:AD:DP:GQ:PL	0/1:17,10:27:99:177,0,472	0/0:26,0:26:0:0,0,478	0/0:31,0:31:0:0,0,511 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.939 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173404 Q155.16 of type=MIXED alleles=[C*, A, CAA] attr={AC=[1, 1], AF=[0.167, 0.167], AN=6, BaseQRankSum=-8.980e-01, ClippingRankSum=0.477, DB=true, DP=71, ExcessHet=3.9794, FS=60.204, MLEAC=[1, 1], MLEAF=[0.167, 0.167], MQ=63.07, MQRankSum=-7.950e-01, QD=3.69, ReadPosRankSum=-1.941e+00, SOR=4.282, VQSLOD=-8.048e+00, culprit=FS} GT=GT:AD:DP:GQ:PL	0/1:8,9,0:17:99:114,0,173,138,198,336	0/0:8,0,0:10:24:0,24,153,24,153,153	0/2:19,0,6:25:58:58,114,584,0,470,451 filters=VQSRTrancheINDEL99.90to99.95
14:32:35.939 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179177312-179177313 Q580.48 of type=INDEL alleles=[CT*, C] attr={AC=4, AF=0.667, AN=6, BaseQRankSum=-4.960e-01, ClippingRankSum=0.996, DB=true, DP=96, ExcessHet=3.6798, FS=24.502, MLEAC=4, MLEAF=0.667, MQ=59.28, MQRankSum=-2.370e-01, POSITIVE_TRAIN_SITE=true, QD=9.67, ReadPosRankSum=0.992, SOR=2.238, VQSLOD=0.814, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/1:3,15:18:0:277,0,0	1/1:1,13:14:31:289,31,0	0/1:23,5:29:26:26,0,379 filters=
14:32:35.939 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179178119-179178120 Q320.25 of type=INDEL alleles=[GT*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-3.200e-02, ClippingRankSum=0.613, DB=true, DP=109, ExcessHet=3.0103, FS=1.824, MLEAC=1, MLEAF=0.167, MQ=59.26, MQRankSum=0.549, QD=13.92, ReadPosRankSum=0.032, SOR=1.473, VQSLOD=0.739, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:72:0,72,936	0/0:42,0:42:56:0,56,1260	0/1:8,15:23:99:329,0,142 filters=
14:32:35.940 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179184000-179184003 Q687.25 of type=INDEL alleles=[TAGA*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-7.160e-01, ClippingRankSum=-1.447e+00, DB=true, DP=107, ExcessHet=3.0103, FS=1.279, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.424, POSITIVE_TRAIN_SITE=true, QD=18.09, ReadPosRankSum=-1.500e-02, SOR=0.976, VQSLOD=2.98, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:78:0,78,1170	0/0:36,0:36:99:0,99,1485	0/1:20,18:38:99:696,0,964 filters=
14:32:35.940 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179187736 Q269.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.02, ClippingRankSum=-1.023e+00, DB=true, DP=58, ExcessHet=3.0103, FS=1.804, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.147e+00, POSITIVE_TRAIN_SITE=true, QD=11.71, ReadPosRankSum=0.031, SOR=1.179, VQSLOD=14.53, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:17,0:17:51:0,51,551	0/0:18,0:18:54:0,54,586	0/1:13,10:23:99:278,0,383 filters=
14:32:35.940 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190789 Q432.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.043e+00, ClippingRankSum=1.94, DB=true, DP=86, ExcessHet=3.0103, FS=10.627, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.513, POSITIVE_TRAIN_SITE=true, QD=12.35, ReadPosRankSum=1.31, SOR=1.991, VQSLOD=17.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:81:0,81,918	0/1:19,16:35:99:441,0,575	0/0:24,0:24:63:0,63,945 filters=
14:32:35.940 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190993 Q526.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.878, ClippingRankSum=-1.700e-02, DB=true, DP=91, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.160e-01, POSITIVE_TRAIN_SITE=true, QD=15.04, ReadPosRankSum=0.248, SOR=0.727, VQSLOD=17.12, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:63:0,63,769	0/0:34,0:34:99:0,102,1142	0/1:16,19:35:99:535,0,431 filters=
14:32:35.941 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179192974 Q4132.69 of type=SNP alleles=[C*, T] attr={AC=6, AF=1.00, AN=6, DB=true, DP=118, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=30.55, SOR=0.781, VQSLOD=20.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1203,99,0	1/1:0,47:47:99:1701,141,0	1/1:0,37:37:99:1242,111,0 filters=
14:32:35.941 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179201626 Q30.26 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-6.480e-01, ClippingRankSum=0.034, DP=80, ExcessHet=3.0103, FS=5.787, MLEAC=1, MLEAF=0.167, MQ=59.33, MQRankSum=0.785, NEGATIVE_TRAIN_SITE=true, QD=1.12, ReadPosRankSum=0.102, SOR=2.799, VQSLOD=-2.303e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:32:0,32,729	0/0:24,0:24:43:0,43,685	0/1:23,4:27:39:39,0,624 filters=VQSRTrancheSNP99.90to100.00
14:32:35.941 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179204486 Q390.25 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.59, ClippingRankSum=-5.460e-01, DB=true, DP=103, ExcessHet=3.0103, FS=1.485, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.768e+00, POSITIVE_TRAIN_SITE=true, QD=13.46, ReadPosRankSum=-1.960e-01, SOR=0.400, VQSLOD=16.40, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1222	0/0:36,0:36:99:0,99,1340	0/1:15,14:29:99:399,0,384 filters=
14:32:35.941 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179205020-179205028 Q89.08 of type=INDEL alleles=[CAAAAAAAA*, C] attr={AC=1, AF=0.250, AN=4, BaseQRankSum=-8.500e-01, ClippingRankSum=0.250, DP=62, ExcessHet=3.9794, FS=2.350, MLEAC=1, MLEAF=0.250, MQ=44.00, MQRankSum=0.050, NEGATIVE_TRAIN_SITE=true, QD=4.69, ReadPosRankSum=0.633, SOR=1.567, VQSLOD=-1.131e+00, culprit=QD} GT=GT:AD:DP:GQ:PL	./.:17,0:17:.:0,0,0	0/1:15,4:19:95:95,0,871	0/0:20,0:20:0:0,0,417 filters=
14:32:35.942 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179206086-179206087 Q139.56 of type=INDEL alleles=[CT*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.204, ClippingRankSum=-1.220e-01, DP=93, ExcessHet=3.0103, FS=1.829, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-4.100e-02, POSITIVE_TRAIN_SITE=true, QD=7.35, ReadPosRankSum=-6.940e-01, SOR=0.976, VQSLOD=2.37, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:96:0,96,1440	0/0:30,0:30:6:0,6,814	0/1:9,10:19:91:148,0,91 filters=
14:32:35.942 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207079 Q2308.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.93, ClippingRankSum=0.350, DB=true, DP=91, ExcessHet=3.0103, FS=1.015, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.590e-01, POSITIVE_TRAIN_SITE=true, QD=25.65, ReadPosRankSum=0.411, SOR=0.479, VQSLOD=17.10, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:1,22:23:34:728,34,0	1/1:0,30:30:90:1020,90,0	0/1:17,20:37:99:575,0,460 filters=
14:32:35.942 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207762 Q438.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.38, ClippingRankSum=-9.390e-01, DB=true, DP=105, ExcessHet=3.0103, FS=3.069, MLEAC=1, MLEAF=0.167, MQ=59.78, MQRankSum=0.143, POSITIVE_TRAIN_SITE=true, QD=12.17, ReadPosRankSum=1.03, SOR=0.293, VQSLOD=1.85, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,102,1257	0/0:33,0:33:99:0,99,1127	0/1:20,16:36:99:447,0,527 filters=
14:32:35.942 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215394 Q561.25 of type=SNP alleles=[T*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.081, ClippingRankSum=0.813, DB=true, DP=110, ExcessHet=3.0103, FS=7.302, MLEAC=1, MLEAF=0.167, MQ=58.66, MQRankSum=2.14, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=14.03, ReadPosRankSum=2.46, SOR=0.153, VQSLOD=-9.316e-01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:29,0:29:81:0,81,1008	0/0:41,0:41:99:0,104,1345	0/1:19,21:40:99:570,0,525 filters=
14:32:35.942 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215575 Q446.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.695, ClippingRankSum=-1.566e+00, DB=true, DP=109, ExcessHet=3.0103, FS=4.093, MLEAC=1, MLEAF=0.167, MQ=55.45, MQRankSum=-5.506e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=9.11, ReadPosRankSum=-3.940e-01, SOR=0.711, VQSLOD=-2.243e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:75:0,75,1125	0/0:32,0:32:90:0,90,1092	0/1:31,18:49:99:455,0,917 filters=
14:32:35.943 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179217522 Q469.25 of type=SNP alleles=[T*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.237, ClippingRankSum=-2.900e-01, DB=true, DP=91, ExcessHet=3.0103, FS=13.704, MLEAC=1, MLEAF=0.167, MQ=56.10, MQRankSum=-2.767e+00, NEGATIVE_TRAIN_SITE=true, QD=18.05, ReadPosRankSum=1.98, SOR=1.947, VQSLOD=-1.277e+00, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:81:0,81,963	0/0:36,0:36:99:0,99,1242	0/1:10,16:26:99:478,0,267 filters=
14:32:35.943 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221303 Q563.25 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.100e-01, ClippingRankSum=1.65, DB=true, DP=117, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=59.98, MQRankSum=0.640, POSITIVE_TRAIN_SITE=true, QD=12.24, ReadPosRankSum=-6.400e-01, SOR=0.719, VQSLOD=3.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:33,0:33:99:0,99,1137	0/0:38,0:38:99:0,103,1236	0/1:25,21:46:99:572,0,731 filters=
14:32:35.943 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221696 Q186.62 of type=INDEL alleles=[C*, CT] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-1.580e-01, ClippingRankSum=1.42, DP=90, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=55.26, MQRankSum=-1.580e-01, QD=16.97, ReadPosRankSum=0.474, SOR=0.399, VQSLOD=2.59, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:27,0:27:7:0,7,730	0/0:32,0:32:26:0,26,912	1/1:1,10:11:22:203,22,0 filters=
14:32:35.943 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179224643 Q334.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.002e+00, ClippingRankSum=-1.038e+00, DB=true, DP=93, ExcessHet=3.0103, FS=1.410, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.100e-01, POSITIVE_TRAIN_SITE=true, QD=10.13, ReadPosRankSum=0.637, SOR=1.193, VQSLOD=16.65, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:63:0,63,945	0/0:36,0:36:99:0,99,1267	0/1:19,14:33:99:343,0,552 filters=
14:32:35.944 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179226199 Q4465.73 of type=INDEL alleles=[T*, TACTTG] attr={AC=6, AF=1.00, AN=6, DB=true, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=32.58, SOR=0.870, VQSLOD=4.17, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,26:26:84:1244,84,0	1/1:0,37:37:99:1684,117,0	1/1:0,33:33:99:1551,105,0 filters=
14:32:35.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179231630 Q153.90 of type=INDEL alleles=[C*, CT] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=-9.670e-01, ClippingRankSum=1.18, DP=78, ExcessHet=0.4576, FS=7.782, MLEAC=1, MLEAF=0.167, MQ=55.92, MQRankSum=-1.182e+00, NEGATIVE_TRAIN_SITE=true, QD=12.83, ReadPosRankSum=0.107, SOR=4.804, VQSLOD=-2.689e+00, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:31:0,31,634	0/0:37,0:37:76:0,76,1115	1/1:2,10:12:3:165,3,0 filters=
14:32:35.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232352 Q328.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.247e+00, ClippingRankSum=0.488, DB=true, DP=106, ExcessHet=3.0103, FS=5.188, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.284e+00, POSITIVE_TRAIN_SITE=true, QD=9.95, ReadPosRankSum=0.127, SOR=0.910, VQSLOD=16.22, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1291	0/1:18,15:33:99:337,0,547	0/0:37,0:37:99:0,103,1237 filters=
14:32:35.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232509 Q343.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-8.060e-01, ClippingRankSum=-7.700e-02, DB=true, DP=104, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.957e+00, POSITIVE_TRAIN_SITE=true, QD=10.73, ReadPosRankSum=-7.670e-01, SOR=0.818, VQSLOD=16.67, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,102,1227	0/0:35,0:35:99:0,101,1177	0/1:19,13:32:99:352,0,540 filters=
14:32:35.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179236244-179236250 Q753.25 of type=INDEL alleles=[TATTGCC*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.77, ClippingRankSum=0.139, DB=true, DP=101, ExcessHet=3.0103, FS=4.716, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.670e-01, POSITIVE_TRAIN_SITE=true, QD=17.93, ReadPosRankSum=0.419, SOR=1.532, VQSLOD=1.73, culprit=SOR} GT=GT:AD:DP:GQ:PL	0/0:24,0:24:69:0,69,1035	0/0:35,0:35:99:0,99,1485	0/1:22,20:42:99:762,0,1723 filters=
14:32:35.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179242400-179242401 Q224.25 of type=INDEL alleles=[GA*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=2.17, ClippingRankSum=0.952, DB=true, DP=93, ExcessHet=3.0103, FS=1.574, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.244e+00, QD=8.31, ReadPosRankSum=2.03, SOR=1.270, VQSLOD=-1.078e-01, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:55:0,55,903	0/0:32,0:32:90:0,90,1350	0/1:15,12:27:99:233,0,310 filters=
14:32:35.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179243192 Q478.25 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.15, ClippingRankSum=-8.050e-01, DB=true, DP=65, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=35.48, MQRankSum=0.595, POSITIVE_TRAIN_SITE=true, QD=20.79, ReadPosRankSum=-5.250e-01, SOR=1.061, VQSLOD=-7.350e+00, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,680	0/0:21,0:21:60:0,60,900	0/1:6,17:23:99:487,0,133 filters=VQSRTrancheSNP99.90to100.00+
14:32:35.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244582 Q498.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.270e-01, ClippingRankSum=1.17, DB=true, DP=92, ExcessHet=3.0103, FS=19.592, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.330e-01, POSITIVE_TRAIN_SITE=true, QD=15.10, ReadPosRankSum=0.524, SOR=0.831, VQSLOD=17.78, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:28,0:28:78:0,78,1170	0/0:31,0:31:90:0,90,1017	0/1:15,18:33:99:507,0,377 filters=
14:32:35.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244703 Q365.29 of type=INDEL alleles=[G*, GA] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-8.890e-01, ClippingRankSum=1.68, DB=true, DP=86, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-2.170e-01, QD=11.78, ReadPosRankSum=0.138, SOR=0.582, VQSLOD=3.58, culprit=FS} GT=GT:AD:DP:GQ:PL	0/0:19,0:19:54:0,54,810	0/0:32,0:32:71:0,71,1003	0/1:15,16:31:99:374,0,299 filters=
14:32:35.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179246281 Q488.25 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.206, ClippingRankSum=0.997, DB=true, DP=98, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-2.060e-01, POSITIVE_TRAIN_SITE=true, QD=13.56, ReadPosRankSum=-3.320e-01, SOR=0.914, VQSLOD=16.84, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:26,0:26:72:0,72,1080	0/0:35,0:35:99:0,105,1216	0/1:18,18:36:99:497,0,477 filters=
14:32:35.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179247445 Q219.25 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.988, ClippingRankSum=-3.040e-01, DB=true, DP=67, ExcessHet=3.0103, FS=7.574, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-3.040e-01, POSITIVE_TRAIN_SITE=true, QD=10.96, ReadPosRankSum=-7.600e-02, SOR=1.182, VQSLOD=15.60, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:19,0:19:51:0,51,765	0/0:27,0:27:72:0,72,1080	0/1:11,9:20:99:228,0,293 filters=
14:32:35.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249007 Q176.29 of type=INDEL alleles=[C*, CT] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.398, ClippingRankSum=-1.810e-01, DP=93, ExcessHet=3.0103, FS=14.970, MLEAC=1, MLEAF=0.167, MQ=59.54, MQRankSum=1.27, NEGATIVE_TRAIN_SITE=true, QD=8.39, ReadPosRankSum=-3.078e+00, SOR=2.047, VQSLOD=-1.813e+00, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	0/0:22,0:22:41:0,41,664	0/0:35,0:35:55:0,55,1006	0/1:8,13:21:92:185,0,92 filters=
14:32:35.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249792 Q281.25 of type=SNP alleles=[A*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-1.217e+00, ClippingRankSum=0.116, DB=true, DP=94, ExcessHet=3.0103, FS=1.660, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-6.370e-01, POSITIVE_TRAIN_SITE=true, QD=11.72, ReadPosRankSum=-1.680e+00, SOR=0.591, VQSLOD=16.74, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:37,0:37:99:0,111,1246	0/0:32,0:32:81:0,81,1215	0/1:13,11:24:99:290,0,380 filters=
14:32:35.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249918 Q476.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=2.23, ClippingRankSum=-6.440e-01, DB=true, DP=82, ExcessHet=3.0103, FS=3.012, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-9.080e-01, POSITIVE_TRAIN_SITE=true, QD=13.61, ReadPosRankSum=1.80, SOR=1.371, VQSLOD=16.16, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:23,0:23:63:0,63,945	0/0:24,0:24:72:0,72,764	0/1:18,17:35:99:485,0,466 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250038 Q3005.69 of type=SNP alleles=[C*, T] attr={AC=6, AF=1.00, AN=6, DB=true, DP=92, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=33.77, SOR=0.809, VQSLOD=21.51, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1078,93,0	1/1:0,27:27:81:919,81,0	1/1:0,31:31:93:1022,93,0 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250846 Q392.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.082, ClippingRankSum=-5.200e-01, DB=true, DP=97, ExcessHet=3.0103, FS=3.831, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.137, POSITIVE_TRAIN_SITE=true, QD=15.69, ReadPosRankSum=-2.700e-02, SOR=0.180, VQSLOD=17.01, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:30,0:30:81:0,81,1215	0/0:41,0:41:99:0,105,1406	0/1:11,14:25:99:401,0,307 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179250872 Q279.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.094, ClippingRankSum=0.329, DB=true, DP=97, ExcessHet=3.0103, FS=6.451, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=0.282, POSITIVE_TRAIN_SITE=true, QD=9.97, ReadPosRankSum=0.376, SOR=2.303, VQSLOD=18.22, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:93:0,93,1153	0/0:36,0:36:99:0,102,1475	0/1:17,11:28:99:288,0,497 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251319 Q1399.10 of type=SNP alleles=[G*, A] attr={AC=2, AF=0.333, AN=6, DB=true, DP=105, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=33.31, SOR=0.693, VQSLOD=22.21, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:31,0:31:90:0,90,1082	0/0:30,0:30:81:0,81,1215	1/1:0,42:42:99:1416,126,0 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251568-179251569 Q272.25 of type=INDEL alleles=[GC*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=0.317, ClippingRankSum=-4.010e-01, DB=true, DP=88, ExcessHet=3.0103, FS=1.523, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.900e-01, POSITIVE_TRAIN_SITE=true, QD=8.78, ReadPosRankSum=-1.078e+00, SOR=1.030, VQSLOD=2.16, culprit=QD} GT=GT:AD:DP:GQ:PL	0/0:29,0:29:81:0,81,1215	0/0:27,0:27:81:0,81,878	0/1:21,10:31:99:281,0,691 filters=
14:32:35.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251754 Q1075.10 of type=SNP alleles=[A*, G] attr={AC=2, AF=0.333, AN=6, DB=true, DP=103, ExcessHet=0.4576, FS=0.000, MLEAC=2, MLEAF=0.333, MQ=59.49, POSITIVE_TRAIN_SITE=true, QD=32.58, SOR=1.022, VQSLOD=4.57, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:32,0:32:90:0,90,1350	0/0:38,0:38:99:0,108,1620	1/1:0,33:33:99:1092,99,0 filters=
14:32:35.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251923 Q474.25 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=1.02, ClippingRankSum=0.707, DB=true, DP=102, ExcessHet=3.0103, FS=7.891, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=-1.570e+00, POSITIVE_TRAIN_SITE=true, QD=13.95, ReadPosRankSum=-9.830e-01, SOR=1.806, VQSLOD=16.71, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:33,0:33:99:0,99,1107	0/0:35,0:35:99:0,99,1211	0/1:16,18:34:99:483,0,433 filters=
14:32:35.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179251953 Q461.25 of type=SNP alleles=[C*, G] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-2.640e-01, ClippingRankSum=-6.420e-01, DB=true, DP=101, ExcessHet=3.0103, FS=8.162, MLEAC=1, MLEAF=0.167, MQ=60.00, MQRankSum=1.21, POSITIVE_TRAIN_SITE=true, QD=14.41, ReadPosRankSum=1.25, SOR=1.646, VQSLOD=16.99, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:34,0:34:99:0,102,1152	0/0:35,0:35:99:0,99,1211	0/1:15,17:32:99:470,0,425 filters=
14:32:35.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179252222 Q2788.69 of type=SNP alleles=[A*, G] attr={AC=6, AF=1.00, AN=6, DB=true, DP=89, ExcessHet=3.0103, FS=0.000, MLEAC=6, MLEAF=1.00, MQ=60.00, POSITIVE_TRAIN_SITE=true, QD=32.43, SOR=1.005, VQSLOD=21.87, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,20:20:59:635,59,0	1/1:0,31:31:93:1007,93,0	1/1:0,35:35:99:1160,105,0 filters=
14:32:35.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253641 Q2275.89 of type=SNP alleles=[C*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.56, ClippingRankSum=0.971, DB=true, DP=86, ExcessHet=3.0103, FS=10.506, MLEAC=5, MLEAF=0.833, MQ=59.96, MQRankSum=-2.430e-01, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=26.78, ReadPosRankSum=0.451, SOR=0.353, VQSLOD=0.342, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,19:19:57:630,57,0	1/1:0,32:32:96:1122,96,0	0/1:15,19:34:99:538,0,399 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179253762 Q2586.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.720e-01, ClippingRankSum=-1.338e+00, DB=true, DP=114, ExcessHet=3.0103, FS=1.962, MLEAC=5, MLEAF=0.833, MQ=59.77, MQRankSum=-5.780e-01, POSITIVE_TRAIN_SITE=true, QD=24.18, ReadPosRankSum=0.352, SOR=0.768, VQSLOD=1.82, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,22:22:66:689,66,0	1/1:0,46:46:99:1468,137,0	0/1:21,18:39:99:444,0,603 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255161 Q3392.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.013e+00, ClippingRankSum=-1.013e+00, DB=true, DP=98, ExcessHet=3.0103, FS=6.010, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=0.184, QD=30.63, ReadPosRankSum=1.38, SOR=0.243, VQSLOD=1.03, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:179255161_T_G:1412,99,0	1/1:0,34:34:99:1|1:179255161_T_G:1451,102,0	0/1:13,15:28:99:0|1:179255161_T_G:544,0,490 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255164 Q3782.93 of type=INDEL alleles=[C*, CA] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.380e-01, ClippingRankSum=0.369, DB=true, DP=95, ExcessHet=3.0103, FS=2.545, MLEAC=5, MLEAF=0.833, MQ=59.82, MQRankSum=0.737, QD=28.90, ReadPosRankSum=0.921, SOR=0.383, VQSLOD=1.64, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,29:29:99:1|1:179255161_T_G:1513,105,0	1/1:0,35:35:99:1|1:179255161_T_G:1701,120,0	0/1:13,15:28:99:0|1:179255161_T_G:583,0,529 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255188 Q3232.89 of type=SNP alleles=[C*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.417, ClippingRankSum=-5.760e-01, DB=true, DP=98, ExcessHet=3.0103, FS=5.267, MLEAC=5, MLEAF=0.833, MQ=59.69, MQRankSum=-7.740e-01, POSITIVE_TRAIN_SITE=true, QD=34.76, ReadPosRankSum=0.695, SOR=0.293, VQSLOD=1.04, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,28:28:87:1|1:179255161_T_G:1264,87,0	1/1:0,34:34:99:1|1:179255161_T_G:1483,105,0	0/1:17,14:31:99:0|1:179255161_T_G:500,0,611 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255255 Q2636.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.850e-01, ClippingRankSum=0.982, DB=true, DP=102, ExcessHet=3.0103, FS=3.573, MLEAC=5, MLEAF=0.833, MQ=59.86, MQRankSum=0.032, POSITIVE_TRAIN_SITE=true, QD=26.64, ReadPosRankSum=0.095, SOR=1.109, VQSLOD=1.51, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:99:1146,99,0	1/1:0,30:30:90:1044,90,0	0/1:19,17:36:99:461,0,551 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255327 Q2558.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.44, ClippingRankSum=1.34, DB=true, DP=106, ExcessHet=3.0103, FS=0.990, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.53, POSITIVE_TRAIN_SITE=true, QD=24.84, ReadPosRankSum=1.63, SOR=0.540, VQSLOD=16.52, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,33:33:98:1067,98,0	1/1:1,34:35:94:1062,94,0	0/1:17,18:35:99:444,0,476 filters=
14:32:35.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179255934 Q3076.89 of type=SNP alleles=[A*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.408e+00, ClippingRankSum=0.974, DB=true, DP=111, ExcessHet=3.0103, FS=5.748, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-9.430e-01, POSITIVE_TRAIN_SITE=true, QD=28.23, ReadPosRankSum=1.72, SOR=0.391, VQSLOD=16.36, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1123,96,0	1/1:0,40:40:99:1355,120,0	0/1:15,22:37:99:613,0,410 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256242 Q2259.89 of type=SNP alleles=[A*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-8.490e-01, ClippingRankSum=-3.150e-01, DB=true, DP=82, ExcessHet=3.0103, FS=4.103, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.315, QD=27.56, ReadPosRankSum=-1.674e+00, SOR=0.307, VQSLOD=14.94, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,19:19:57:671,57,0	1/1:0,36:36:99:1262,108,0	0/1:14,13:27:99:341,0,395 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256462 Q2630.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.160e-01, ClippingRankSum=0.546, DB=true, DP=103, ExcessHet=3.0103, FS=3.519, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-2.480e-01, POSITIVE_TRAIN_SITE=true, QD=26.31, ReadPosRankSum=1.80, SOR=0.335, VQSLOD=16.39, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,28:28:84:953,84,0	1/1:0,37:37:99:1241,111,0	0/1:19,16:35:99:451,0,500 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179256883 Q2600.89 of type=SNP alleles=[A*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.811, ClippingRankSum=-4.060e-01, DB=true, DP=88, ExcessHet=3.0103, FS=8.554, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-1.217e+00, POSITIVE_TRAIN_SITE=true, QD=29.56, ReadPosRankSum=1.85, SOR=0.525, VQSLOD=15.87, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1316,111,0	1/1:0,27:27:81:989,81,0	0/1:13,11:24:99:310,0,370 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257051 Q2339.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.493, ClippingRankSum=0.080, DB=true, DP=94, ExcessHet=3.0103, FS=9.170, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-4.800e-02, POSITIVE_TRAIN_SITE=true, QD=25.16, ReadPosRankSum=-7.800e-01, SOR=1.446, VQSLOD=16.26, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:859,75,0	1/1:0,32:32:96:1082,96,0	0/1:20,16:36:99:413,0,567 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257184 Q2329.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.500e-02, ClippingRankSum=1.06, DB=true, DP=87, ExcessHet=3.0103, FS=2.290, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.73, POSITIVE_TRAIN_SITE=true, QD=26.78, ReadPosRankSum=0.353, SOR=0.598, VQSLOD=15.91, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,21:21:63:738,63,0	1/1:0,29:29:87:1006,87,0	0/1:16,21:37:99:600,0,445 filters=
14:32:35.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257620 Q2638.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.710e-01, ClippingRankSum=0.416, DB=true, DP=105, ExcessHet=3.0103, FS=3.442, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.70, POSITIVE_TRAIN_SITE=true, QD=25.37, ReadPosRankSum=-1.318e+00, SOR=0.600, VQSLOD=16.50, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:819,75,0	1/1:0,45:45:99:1484,134,0	0/1:19,15:34:99:350,0,539 filters=
14:32:35.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257738 Q3124.89 of type=SNP alleles=[G*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.19, ClippingRankSum=0.766, DB=true, DP=99, ExcessHet=3.0103, FS=1.985, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.50, POSITIVE_TRAIN_SITE=true, QD=31.89, ReadPosRankSum=0.00, SOR=0.897, VQSLOD=15.63, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,19:19:60:1|1:179257738_G_T:880,60,0	1/1:0,39:39:99:1|1:179257738_G_T:1669,117,0	0/1:23,17:40:99:0|1:179257738_G_T:590,0,1285 filters=
14:32:35.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257767 Q3199.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.19, ClippingRankSum=-3.220e-01, DB=true, DP=100, ExcessHet=3.0103, FS=2.068, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-7.200e-01, POSITIVE_TRAIN_SITE=true, QD=32.99, ReadPosRankSum=-8.430e-01, SOR=0.922, VQSLOD=15.62, culprit=MQ} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,22:22:69:1|1:179257738_G_T:994,69,0	1/1:0,38:38:99:1|1:179257738_G_T:1652,117,0	0/1:21,16:37:99:0|1:179257738_G_T:568,0,1203 filters=
14:32:35.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257889-179257890 Q3069.89 of type=INDEL alleles=[TG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.155, ClippingRankSum=-6.600e-02, DP=94, ExcessHet=3.0103, FS=2.196, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.952, QD=33.74, ReadPosRankSum=0.199, SOR=0.462, VQSLOD=1.53, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,21:21:63:1|1:179257889_TG_T:901,63,0	1/1:0,41:41:99:1|1:179257889_TG_T:1761,124,0	0/1:17,12:29:99:0|1:179257889_TG_T:422,0,1693 filters=
14:32:35.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257891-179257898 Q3063.89 of type=INDEL alleles=[TGTGTGTG*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.783, ClippingRankSum=1.16, DB=true, DP=95, ExcessHet=3.0103, FS=2.220, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.275, QD=33.30, ReadPosRankSum=-2.300e-02, SOR=0.401, VQSLOD=1.59, culprit=QD} GT=GT:AD:DP:GQ:PGT:PID:PL	1/1:0,21:21:63:1|1:179257889_TG_T:901,63,0	1/1:0,41:41:99:1|1:179257889_TG_T:1761,124,0	0/1:18,12:30:99:0|1:179257889_TG_T:416,0,1755 filters=
14:32:35.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258111 Q2662.89 of type=SNP alleles=[T*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.39, ClippingRankSum=1.31, DB=true, DP=100, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.94, MQRankSum=1.65, POSITIVE_TRAIN_SITE=true, QD=27.45, ReadPosRankSum=0.661, SOR=0.611, VQSLOD=3.65, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,25:25:75:844,75,0	1/1:1,40:41:99:1336,99,0	0/1:13,18:31:99:497,0,359 filters=
14:32:35.953 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258178 Q2710.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-6.520e-01, ClippingRankSum=-1.166e+00, DB=true, DP=103, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.78, MQRankSum=-5.730e-01, QD=26.58, ReadPosRankSum=2.12, SOR=0.698, VQSLOD=3.34, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1037,96,0	1/1:0,39:39:99:1280,116,0	0/1:16,15:31:99:408,0,463 filters=
14:32:35.953 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258390 Q2940.89 of type=SNP alleles=[A*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.830e-01, ClippingRankSum=0.886, DB=true, DP=106, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-3.580e-01, POSITIVE_TRAIN_SITE=true, QD=27.74, ReadPosRankSum=0.433, SOR=0.646, VQSLOD=17.14, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1079,96,0	1/1:0,42:42:99:1416,126,0	0/1:16,16:32:99:460,0,435 filters=
14:32:35.953 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258419 Q2608.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-9.400e-02, ClippingRankSum=0.773, DB=true, DP=101, ExcessHet=3.0103, FS=1.047, MLEAC=5, MLEAF=0.833, MQ=59.88, MQRankSum=-6.970e-01, POSITIVE_TRAIN_SITE=true, QD=26.09, ReadPosRankSum=0.320, SOR=0.552, VQSLOD=2.41, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,27:27:81:853,81,0	1/1:0,41:41:99:1330,123,0	0/1:16,16:32:99:440,0,460 filters=
14:32:35.953 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258803 Q2882.89 of type=SNP alleles=[T*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.135, ClippingRankSum=-1.571e+00, DB=true, DP=105, ExcessHet=3.0103, FS=3.332, MLEAC=5, MLEAF=0.833, MQ=59.82, MQRankSum=2.49, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=27.46, ReadPosRankSum=2.00, SOR=0.346, VQSLOD=1.04, culprit=MQRankSum} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1344,111,0	1/1:0,28:28:84:1023,84,0	0/1:21,19:40:99:530,0,589 filters=
14:32:35.953 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258989 Q2795.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.076, ClippingRankSum=0.717, DB=true, DP=99, ExcessHet=3.0103, FS=0.000, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-9.820e-01, POSITIVE_TRAIN_SITE=true, QD=28.53, ReadPosRankSum=-8.690e-01, SOR=0.603, VQSLOD=3.70, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,35:35:99:1237,105,0	1/1:0,31:31:93:1108,93,0	0/1:15,17:32:99:465,0,423 filters=
14:32:35.954 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179259033 Q2966.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.86, ClippingRankSum=-1.301e+00, DB=true, DP=100, ExcessHet=3.0103, FS=1.111, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-9.810e-01, QD=29.97, ReadPosRankSum=-7.810e-01, SOR=0.621, VQSLOD=1.10, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,40:40:99:1410,120,0	1/1:0,28:28:84:1048,84,0	0/1:13,18:31:99:523,0,359 filters=
14:32:35.954 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179259323 Q3040.89 of type=SNP alleles=[G*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.900e-01, ClippingRankSum=-7.900e-02, DB=true, DP=103, ExcessHet=3.0103, FS=7.231, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-1.713e+00, POSITIVE_TRAIN_SITE=true, QD=29.81, ReadPosRankSum=0.712, SOR=0.505, VQSLOD=16.01, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,34:34:99:1147,102,0	1/1:0,42:42:99:1460,126,0	0/1:10,16:26:99:448,0,269 filters=
14:32:35.954 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260056 Q2404.89 of type=SNP alleles=[G*, C] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.832, ClippingRankSum=1.46, DB=true, DP=89, ExcessHet=3.0103, FS=7.907, MLEAC=5, MLEAF=0.833, MQ=59.78, MQRankSum=-1.041e+00, POSITIVE_TRAIN_SITE=true, QD=27.33, ReadPosRankSum=0.902, SOR=0.561, VQSLOD=1.54, culprit=FS} GT=GT:AD:DP:GQ:PL	1/1:0,23:23:69:799,69,0	1/1:0,31:31:93:1097,93,0	0/1:15,19:34:99:523,0,400 filters=
14:32:35.954 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260290 Q2662.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.500, ClippingRankSum=-1.960e-01, DB=true, DP=90, ExcessHet=3.0103, FS=1.458, MLEAC=5, MLEAF=0.833, MQ=59.83, MQRankSum=-1.327e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=29.92, ReadPosRankSum=2.02, SOR=0.383, VQSLOD=1.29, culprit=QD} GT=GT:AD:DP:GQ:PL	1/1:0,28:28:84:943,84,0	1/1:0,29:29:87:996,87,0	0/1:8,24:32:99:738,0,182 filters=
14:32:35.954 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260540 Q3121.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=2.63, ClippingRankSum=0.380, DB=true, DP=108, ExcessHet=3.0103, FS=5.368, MLEAC=5, MLEAF=0.833, MQ=59.61, MQRankSum=-1.553e+00, NEGATIVE_TRAIN_SITE=true, POSITIVE_TRAIN_SITE=true, QD=28.91, ReadPosRankSum=-1.775e+00, SOR=0.458, VQSLOD=0.718, culprit=ReadPosRankSum} GT=GT:AD:DP:GQ:PL	1/1:0,30:30:90:1133,90,0	1/1:0,42:42:99:1450,126,0	0/1:17,19:36:99:553,0,413 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260754 Q3003.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.208, ClippingRankSum=1.56, DB=true, DP=106, ExcessHet=3.0103, FS=3.942, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=0.727, POSITIVE_TRAIN_SITE=true, QD=28.34, ReadPosRankSum=0.467, SOR=0.675, VQSLOD=16.45, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,37:37:99:1275,111,0	1/1:0,43:43:99:1464,129,0	0/1:15,11:26:99:279,0,444 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260816 Q2359.89 of type=SNP alleles=[T*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-1.402e+00, ClippingRankSum=-7.350e-01, DB=true, DP=91, ExcessHet=3.0103, FS=1.158, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-6.680e-01, POSITIVE_TRAIN_SITE=true, QD=25.93, ReadPosRankSum=-8.680e-01, SOR=0.750, VQSLOD=16.47, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,31:31:93:1017,93,0	1/1:0,38:38:99:1180,112,0	0/1:13,9:22:99:177,0,376 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260901 Q2768.89 of type=SNP alleles=[A*, G] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=0.025, ClippingRankSum=0.666, DB=true, DP=97, ExcessHet=3.0103, FS=4.486, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=-7.650e-01, POSITIVE_TRAIN_SITE=true, QD=28.55, ReadPosRankSum=-7.650e-01, SOR=0.464, VQSLOD=16.16, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1057,96,0	1/1:0,38:38:99:1286,114,0	0/1:11,16:27:99:440,0,272 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260930 Q2820.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-7.470e-01, ClippingRankSum=0.346, DB=true, DP=104, ExcessHet=3.0103, FS=5.049, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=1.26, POSITIVE_TRAIN_SITE=true, QD=27.12, ReadPosRankSum=1.55, SOR=0.800, VQSLOD=15.85, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,32:32:96:1092,96,0	1/1:0,39:39:99:1356,117,0	0/1:19,14:33:99:387,0,551 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262286 Q517.25 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.167, AN=6, BaseQRankSum=-4.900e-02, ClippingRankSum=-8.900e-01, DP=111, ExcessHet=3.0103, FS=3.836, MLEAC=1, MLEAF=0.167, MQ=59.93, MQRankSum=-9.380e-01, QD=8.92, ReadPosRankSum=0.210, SOR=1.276, VQSLOD=-9.570e-02, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/0:18,0:18:51:0,51,765	0/0:35,0:35:99:0,99,1235	0/1:37,21:58:99:526,0,1082 filters=
14:32:35.955 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262480 Q2208.89 of type=SNP alleles=[G*, A] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=-2.430e-01, ClippingRankSum=-5.800e-02, DB=true, DP=95, ExcessHet=3.0103, FS=3.148, MLEAC=5, MLEAF=0.833, MQ=60.00, MQRankSum=2.00, POSITIVE_TRAIN_SITE=true, QD=23.25, ReadPosRankSum=0.405, SOR=0.414, VQSLOD=16.20, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:0,21:21:63:730,63,0	1/1:0,29:29:87:1003,87,0	0/1:27,18:45:99:490,0,763 filters=
14:32:35.956 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262545 Q2541.89 of type=SNP alleles=[C*, T] attr={AC=5, AF=0.833, AN=6, BaseQRankSum=1.79, ClippingRankSum=0.065, DB=true, DP=112, ExcessHet=3.0103, FS=3.965, MLEAC=5, MLEAF=0.833, MQ=59.93, MQRankSum=0.116, POSITIVE_TRAIN_SITE=true, QD=23.11, ReadPosRankSum=0.578, SOR=0.384, VQSLOD=1.95, culprit=MQ} GT=GT:AD:DP:GQ:PL	1/1:1,29:30:80:978,80,0	1/1:0,32:32:96:1142,96,0	0/1:31,17:48:99:436,0,883 filters=
14:32:35.956 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179262851 Q766.12 of type=SNP alleles=[G*, A] attr={AC=2, AF=0.333, AN=6, BaseQRankSum=0.812, ClippingRankSum=1.18, DB=true, DP=92, ExcessHet=3.9794, FS=1.012, MLEAC=2, MLEAF=0.333, MQ=59.92, MQRankSum=-6.730e-01, POSITIVE_TRAIN_SITE=true, QD=13.44, ReadPosRankSum=1.42, SOR=0.922, VQSLOD=1.58, culprit=MQ} GT=GT:AD:DP:GQ:PL	0/1:14,15:29:99:454,0,399	0/1:16,12:28:99:323,0,447	0/0:34,0:34:88:0,88,1082 filters=
14:32:35.956 INFO  ProgressMeter -             unmapped              0.0                   100         200000.0
14:32:35.956 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:32:35.956 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:32:35.956 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:35.957 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out10459218168317404333.vcf
14:32:36.115 INFO  Funcotator - ------------------------------------------------------------
14:32:36.116 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:36.116 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:36.116 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:36.116 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:36.116 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:36 PM GMT
14:32:36.116 INFO  Funcotator - ------------------------------------------------------------
14:32:36.116 INFO  Funcotator - ------------------------------------------------------------
14:32:36.116 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:36.116 INFO  Funcotator - Picard Version: 3.4.0
14:32:36.116 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:36.116 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:36.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:36.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:36.116 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:36.116 INFO  Funcotator - Deflater: IntelDeflater
14:32:36.116 INFO  Funcotator - Inflater: IntelInflater
14:32:36.116 INFO  Funcotator - GCS max retries/reopens: 20
14:32:36.116 INFO  Funcotator - Requester pays: disabled
14:32:36.116 INFO  Funcotator - Initializing engine
14:32:36.117 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:32:36.117 INFO  Funcotator - Done initializing engine
14:32:36.117 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:36.117 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:36.117 INFO  Funcotator - Initializing data sources...
14:32:36.117 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:32:36.117 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:36.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.118 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:36.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.118 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:36.118 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.119 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.119 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:32:36.119 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.120 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.121 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.122 INFO  Funcotator - Initializing Funcotator Engine...
14:32:36.122 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:32:36.122 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:32:36.122 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:32:36.122 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6742018242108263973.vcf
14:32:36.123 INFO  ProgressMeter - Starting traversal
14:32:36.123 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:36.153 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
14:32:36.153 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:32:36.153 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:32:36.155 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:36.242 INFO  Funcotator - ------------------------------------------------------------
14:32:36.242 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:36.242 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:36.242 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:36.242 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:36.242 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:36 PM GMT
14:32:36.242 INFO  Funcotator - ------------------------------------------------------------
14:32:36.242 INFO  Funcotator - ------------------------------------------------------------
14:32:36.242 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:36.242 INFO  Funcotator - Picard Version: 3.4.0
14:32:36.242 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:36.242 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:36.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:36.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:36.242 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:36.242 INFO  Funcotator - Deflater: IntelDeflater
14:32:36.242 INFO  Funcotator - Inflater: IntelInflater
14:32:36.242 INFO  Funcotator - GCS max retries/reopens: 20
14:32:36.242 INFO  Funcotator - Requester pays: disabled
14:32:36.242 INFO  Funcotator - Initializing engine
14:32:36.243 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:32:36.243 INFO  Funcotator - Done initializing engine
14:32:36.243 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:36.243 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:36.243 INFO  Funcotator - Initializing data sources...
14:32:36.243 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:32:36.243 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:36.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.244 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:36.244 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.244 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:36.245 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.245 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.245 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.245 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:32:36.246 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.246 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.247 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.248 INFO  Funcotator - Initializing Funcotator Engine...
14:32:36.248 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:32:36.248 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:32:36.248 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:32:36.248 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5054641832616301931.maf
14:32:36.248 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:32:36.249 INFO  ProgressMeter - Starting traversal
14:32:36.249 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:36.251 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
14:32:36.251 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
14:32:36.252 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
14:32:36.252 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:32:36.254 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
14:32:36.254 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
14:32:36.254 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:32:36.255 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
14:32:36.255 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:32:36.256 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:32:36.256 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:32:36.256 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:32:36.257 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
14:32:36.258 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
14:32:36.258 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
14:32:36.259 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
14:32:36.259 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
14:32:36.260 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
14:32:36.260 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
14:32:36.260 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
14:32:36.262 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:32:36.262 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
14:32:36.263 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
14:32:36.264 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:32:36.264 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
14:32:36.265 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:32:36.266 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
14:32:36.267 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
14:32:36.267 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:32:36.268 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:32:36.268 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:32:36.269 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:32:36.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:32:36.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:32:36.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
14:32:36.271 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
14:32:36.272 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:32:36.273 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
14:32:36.273 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
14:32:36.274 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
14:32:36.274 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
14:32:36.275 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
14:32:36.276 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
14:32:36.276 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
14:32:36.276 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
14:32:36.278 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
14:32:36.278 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
14:32:36.278 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
14:32:36.279 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
14:32:36.280 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
14:32:36.280 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
14:32:36.281 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
14:32:36.281 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
14:32:36.282 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
14:32:36.283 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
14:32:36.283 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
14:32:36.283 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
14:32:36.283 INFO  ProgressMeter -             unmapped              0.0                    57         100588.2
14:32:36.283 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:32:36.283 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:32:36.284 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:36.285 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6742018242108263973.vcf
14:32:36.409 INFO  Funcotator - ------------------------------------------------------------
14:32:36.409 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:36.409 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:36.409 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:36.409 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:36.409 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:36 PM GMT
14:32:36.409 INFO  Funcotator - ------------------------------------------------------------
14:32:36.409 INFO  Funcotator - ------------------------------------------------------------
14:32:36.409 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:36.409 INFO  Funcotator - Picard Version: 3.4.0
14:32:36.409 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:36.409 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:36.409 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:36.409 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:36.409 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:36.409 INFO  Funcotator - Deflater: IntelDeflater
14:32:36.409 INFO  Funcotator - Inflater: IntelInflater
14:32:36.409 INFO  Funcotator - GCS max retries/reopens: 20
14:32:36.409 INFO  Funcotator - Requester pays: disabled
14:32:36.409 INFO  Funcotator - Initializing engine
14:32:36.410 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:32:36.411 INFO  Funcotator - Done initializing engine
14:32:36.411 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:36.411 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:36.411 INFO  Funcotator - Initializing data sources...
14:32:36.411 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:32:36.411 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:36.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.412 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:36.412 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.412 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:36.412 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.412 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.413 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.413 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:32:36.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.414 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.415 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
14:32:36.416 INFO  Funcotator - Initializing Funcotator Engine...
14:32:36.416 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:32:36.416 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:32:36.416 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7978645892351221888.maf
14:32:36.417 INFO  ProgressMeter - Starting traversal
14:32:36.417 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:36.419 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 @ 3:178872355 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.823, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178872355, ILLUMINA_STRAND=TOP, N_AA=4, N_AB=194, N_BB=1053, PROBE_A=AATGTGTTACAATCTGTCCCCCACCATATACATATACAAAGTAGCAGTCC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.02, devTHETA_AB=0.035, devTHETA_BB=0.018, devX_AA=0.095, devX_AB=0.05, devX_BB=0.02, devY_AA=0.022, devY_AB=0.06, devY_BB=0.094, meanR_AA=0.748, meanR_AB=0.789, meanR_BB=0.755, meanTHETA_AA=0.052, meanTHETA_AB=0.569, meanTHETA_BB=0.946, meanX_AA=0.692, meanX_AB=0.352, meanX_BB=0.059, meanY_AA=0.056, meanY_AB=0.437, meanY_BB=0.695, refSNP=rs11706842, zthresh_X=0.18402316111, zthresh_Y=0.185250013887} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.514, GTA=1/0, GTZ=1/0, IGC=0.849, LRR=-0.05, NORMX=0.333, NORMY=0.428, R=0.761, THETA=0.579, X=4554, Y=2131}]] filters=
14:32:36.420 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178902506 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=928, GC_SCORE=0.893, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178902506, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=28, N_BB=1220, PROBE_A=TTATTGGACCAGCCTAGACTGAAAATCTTCTGTTTAGGCATTTTGGTGGG, PROBE_B=., SOURCE=psych, devR_AA=0.1, devR_AB=0.105, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.023, devTHETA_BB=0.01, devX_AA=0.101, devX_AB=0.054, devX_BB=0.015, devY_AA=0.031, devY_AB=0.055, devY_BB=0.097, meanR_AA=0.948, meanR_AB=1.181, meanR_BB=0.994, meanTHETA_AA=0.026, meanTHETA_AB=0.512, meanTHETA_BB=0.973, meanX_AA=0.911, meanX_AB=0.58, meanX_BB=0.041, meanY_AA=0.037, meanY_AB=0.602, meanY_BB=0.953, refSNP=rs111868222, zthresh_X=0.140378981558, zthresh_Y=0.166929562077} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.99, GTA=0/0, GTZ=0/0, IGC=0.882, LRR=0.069, NORMX=0.057, NORMY=0.99, R=1.047, THETA=0.963, X=1498, Y=5593}]] filters=
14:32:36.420 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178907849 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.797, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178907849, ILLUMINA_STRAND=TOP, N_AA=19, N_AB=360, N_BB=872, PROBE_A=GAGGCCCTAACTGGGGCCCAGAAAATTGTACTGAAGGATACTTGCTTCCT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.023, devTHETA_AB=0.038, devTHETA_BB=0.021, devX_AA=0.094, devX_AB=0.05, devX_BB=0.018, devY_AA=0.019, devY_AB=0.056, devY_BB=0.093, meanR_AA=0.556, meanR_AB=0.58, meanR_BB=0.576, meanTHETA_AA=0.054, meanTHETA_AB=0.544, meanTHETA_BB=0.94, meanX_AA=0.513, meanX_AB=0.27, meanX_BB=0.05, meanY_AA=0.043, meanY_AB=0.31, meanY_BB=0.526, refSNP=rs9866361, zthresh_X=0.161949964118, zthresh_Y=0.175918019742} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.978, GTA=0/0, GTZ=0/0, IGC=0.811, LRR=-0.054, NORMX=0.061, NORMY=0.495, R=0.555, THETA=0.922, X=1038, Y=2429}]] filters=
14:32:36.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916753 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.886, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916753, ILLUMINA_STRAND=TOP, N_AA=1247, N_AB=0, N_BB=0, PROBE_A=GATAGTGACTTTAGAATGCCTCCGTGAGGCTACATTAATAACCATAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.094, devX_AB=0.05, devX_BB=0.017, devY_AA=0.015, devY_AB=0.052, devY_BB=0.098, meanR_AA=0.455, meanR_AB=0.541, meanR_BB=0.503, meanTHETA_AA=0.047, meanTHETA_AB=0.511, meanTHETA_BB=0.976, meanX_AA=0.424, meanX_AB=0.266, meanX_BB=0.018, meanY_AA=0.031, meanY_AB=0.275, meanY_BB=0.485, refSNP=rs190372148, zthresh_X=0.182850738152, zthresh_Y=0.12847847542} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.489, LRR=0.114, NORMX=0.459, NORMY=0.034, R=0.493, THETA=0.047, X=8065, Y=228}]] filters=
14:32:36.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916791 Q. of type=SNP alleles=[C*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.89, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178916791, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TAACCATAAAGCATGAACTATTTAAAGAAGCAAGAAAATACCCCCTCCAT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.013, devX_AA=0.099, devX_AB=0.053, devX_BB=0.014, devY_AA=0.024, devY_AB=0.052, devY_BB=0.096, meanR_AA=0.738, meanR_AB=0.886, meanR_BB=0.745, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.965, meanX_AA=0.711, meanX_AB=0.447, meanX_BB=0.039, meanY_AA=0.027, meanY_AB=0.439, meanY_BB=0.706, refSNP=rs71310379, zthresh_X=0.133750336661, zthresh_Y=0.164321280546} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.494, LRR=0.001, NORMX=0.022, NORMY=0.718, R=0.741, THETA=0.98, X=620, Y=4057}]] filters=
14:32:36.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178921158 Q. of type=SNP alleles=[G*, A] attr={AC=1, AF=0.500, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=927, GC_SCORE=0.788, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178921158, ILLUMINA_STRAND=TOP, N_AA=30, N_AB=414, N_BB=807, PROBE_A=CTTTCGTGCAATTTATATTCAGAAGTGTTTGATTGATCTTGTGCTTCAAC, PROBE_B=., SOURCE=dbSNP, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.016, devTHETA_AB=0.029, devTHETA_BB=0.015, devX_AA=0.094, devX_AB=0.049, devX_BB=0.021, devY_AA=0.019, devY_AB=0.061, devY_BB=0.092, meanR_AA=0.827, meanR_AB=0.983, meanR_BB=0.947, meanTHETA_AA=0.05, meanTHETA_AB=0.585, meanTHETA_BB=0.933, meanX_AA=0.767, meanX_AB=0.426, meanX_BB=0.09, meanY_AA=0.06, meanY_AB=0.557, meanY_BB=0.857, refSNP=rs7623154, zthresh_X=0.224662521322, zthresh_Y=0.204527740428} GT=[[0816201804HC0_R01C01 G*/A {BAF=0.484, GTA=1/0, GTZ=1/0, IGC=0.797, LRR=0.017, NORMX=0.442, NORMY=0.547, R=0.99, THETA=0.567, X=6004, Y=2730}]] filters=
14:32:36.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 Q. of type=SNP alleles=[C*, G] attr={AC=0, AF=0.00, ALLELE_A=G, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178922361, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1249, PROBE_A=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACG, PROBE_B=TACCATGGAGGAGAACCCTTATGTGACAATGTGAACACTCAAAGAGTACC, SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.014, devX_AA=0.099, devX_AB=0.052, devX_BB=0.014, devY_AA=0.022, devY_AB=0.052, devY_BB=0.097, meanR_AA=0.664, meanR_AB=0.793, meanR_BB=0.678, meanTHETA_AA=0.024, meanTHETA_AB=0.501, meanTHETA_BB=0.977, meanX_AA=0.64, meanX_AB=0.396, meanX_BB=0.024, meanY_AA=0.025, meanY_AB=0.397, meanY_BB=0.654, refSNP=rs113613074, zthresh_X=0.119568794798, zthresh_Y=0.156845592246} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.515, LRR=-0.048, NORMX=0.015, NORMY=0.639, R=0.654, THETA=0.986, X=603, Y=11188}]] filters=
14:32:36.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=1161, GC_SCORE=0.868, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178927410, ILLUMINA_STRAND=BOT, N_AA=1072, N_AB=169, N_BB=0, PROBE_A=GAGCAAATGGAAAGGCAAAGTCGAGCAGCACGAGGAAGATCAGGAATGTA, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.042, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.058, devX_BB=0.024, devY_AA=0.015, devY_AB=0.059, devY_BB=0.099, meanR_AA=0.829, meanR_AB=0.918, meanR_BB=0.742, meanTHETA_AA=0.017, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=0.808, meanX_AB=0.452, meanX_BB=0.028, meanY_AA=0.021, meanY_AB=0.466, meanY_BB=0.714, refSNP=rs2230461, zthresh_X=0.183044318831, zthresh_Y=0.127662818665} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.009, GTA=0/0, GTZ=0/0, IGC=0.851, LRR=0.267, NORMX=0.961, NORMY=0.038, R=1, THETA=0.025, X=15373, Y=361}]] filters=
14:32:36.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=971, GC_SCORE=0.869, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178932551, ILLUMINA_STRAND=TOP, N_AA=343, N_AB=398, N_BB=479, PROBE_A=GTGAAGACCTGCTGTTTTCTCTGCTTCCAAGCTCAACTAACAATATATTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.131, devR_AB=0.1, devR_BB=0.123, devTHETA_AA=0.017, devTHETA_AB=0.023, devTHETA_BB=0.022, devX_AA=0.126, devX_AB=0.061, devX_BB=0.024, devY_AA=0.017, devY_AB=0.074, devY_BB=0.118, meanR_AA=0.622, meanR_AB=0.938, meanR_BB=0.739, meanTHETA_AA=0.028, meanTHETA_AB=0.563, meanTHETA_BB=0.965, meanX_AA=0.596, meanX_AB=0.423, meanX_BB=0.038, meanY_AA=0.026, meanY_AB=0.515, meanY_BB=0.701, refSNP=rs12494623, zthresh_X=0.152176899827, zthresh_Y=0.170103096568} GT=[[0816201804HC0_R01C01 T/T {BAF=0.027, GTA=1/1, GTZ=1/1, IGC=0.906, LRR=-0.336, NORMX=0.465, NORMY=0.042, R=0.507, THETA=0.057, X=7174, Y=362}]] filters=
14:32:36.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.891, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178937400, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CATACACAGATGTATTGCTTGGTAAAAGATTGGCCTCCAATCAAACCTGA, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.108, devR_BB=0.1, devTHETA_AA=0.013, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.053, devX_BB=0.026, devY_AA=0.015, devY_AB=0.053, devY_BB=0.1, meanR_AA=0.79, meanR_AB=0.96, meanR_BB=0.803, meanTHETA_AA=0.031, meanTHETA_AB=0.503, meanTHETA_BB=0.976, meanX_AA=0.753, meanX_AB=0.477, meanX_BB=0.029, meanY_AA=0.037, meanY_AB=0.482, meanY_BB=0.773, refSNP=rs137902538, zthresh_X=0.187164813479, zthresh_Y=0.140282002247} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.496, LRR=-0.05, NORMX=0.731, NORMY=0.031, R=0.761, THETA=0.027, X=12748, Y=231}]] filters=
14:32:36.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.902, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178947118, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=ACCTTTCAAGCCGCCTTTGCACTGAATTTGCATAATAGTGTGAGAATTTC, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.098, devX_AB=0.052, devX_BB=0.014, devY_AA=0.019, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.576, meanR_AB=0.681, meanR_BB=0.596, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.964, meanX_AA=0.555, meanX_AB=0.344, meanX_BB=0.032, meanY_AA=0.021, meanY_AB=0.337, meanY_BB=0.565, zthresh_X=0.122228724787, zthresh_Y=0.159007429626} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.509, LRR=0.03, NORMX=0.022, NORMY=0.585, R=0.607, THETA=0.977, X=711, Y=3117}]] filters=
14:32:36.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 Q. of type=SNP alleles=[C*, T] attr={AC=2, AF=1.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=927, GC_SCORE=0.848, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178950297, ILLUMINA_STRAND=BOT, N_AA=486, N_AB=560, N_BB=205, PROBE_A=GTCTGTGTGTCTGCTTTTGTGTGTATCTGCTGTTTTGGTAATTATAGTTT, PROBE_B=., SOURCE=dbSNP, devR_AA=0.102, devR_AB=0.12, devR_BB=0.1, devTHETA_AA=0.012, devTHETA_AB=0.028, devTHETA_BB=0.016, devX_AA=0.099, devX_AB=0.057, devX_BB=0.022, devY_AA=0.018, devY_AB=0.057, devY_BB=0.094, meanR_AA=1.064, meanR_AB=1.186, meanR_BB=1.006, meanTHETA_AA=0.03, meanTHETA_AB=0.494, meanTHETA_BB=0.943, meanX_AA=1.016, meanX_AB=0.598, meanX_BB=0.083, meanY_AA=0.048, meanY_AB=0.587, meanY_BB=0.923, refSNP=rs1607237, zthresh_X=0.199217026256, zthresh_Y=0.172626912202} GT=[[0816201804HC0_R01C01 T/T {BAF=0, GTA=1/1, GTZ=1/1, IGC=0.882, LRR=-0.014, NORMX=1.013, NORMY=0.039, R=1.052, THETA=0.025, X=13288, Y=291}]] filters=
14:32:36.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.832, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960744, ILLUMINA_STRAND=BOT, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=AAGATTTCTCTGCTCTTCCTTTGCTCCTCCTCATAATGCACAGTTTGAAC, PROBE_B=., SOURCE=1000_genomes, devR_AA=0.1, devR_AB=0.195, devR_BB=0.113, devTHETA_AA=0.007, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.099, devX_AB=0.059, devX_BB=0.042, devY_AA=0.015, devY_AB=0.058, devY_BB=0.117, meanR_AA=1.388, meanR_AB=1.725, meanR_BB=1.296, meanTHETA_AA=0.014, meanTHETA_AB=0.495, meanTHETA_BB=0.975, meanX_AA=1.358, meanX_AB=0.87, meanX_BB=0.048, meanY_AA=0.029, meanY_AB=0.855, meanY_BB=1.248, refSNP=rs200646413, zthresh_X=0.181538312311, zthresh_Y=0.124907131052} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0.004, GTA=0/0, GTZ=0/0, IGC=0.423, LRR=0.033, NORMX=1.384, NORMY=0.039, R=1.423, THETA=0.018, X=24000, Y=330}]] filters=
14:32:36.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 Q. of type=SNP alleles=[A*, G] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=G, AN=2, BEADSET_ID=850, GC_SCORE=0.847, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178960843, ILLUMINA_STRAND=TOP, N_AA=1251, N_AB=0, N_BB=0, PROBE_A=CAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.18, devR_BB=0.106, devTHETA_AA=0.009, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.096, devX_AB=0.057, devX_BB=0.04, devY_AA=0.017, devY_AB=0.058, devY_BB=0.11, meanR_AA=1.287, meanR_AB=1.594, meanR_BB=1.215, meanTHETA_AA=0.034, meanTHETA_AB=0.505, meanTHETA_BB=0.976, meanX_AA=1.221, meanX_AB=0.791, meanX_BB=0.044, meanY_AA=0.066, meanY_AB=0.804, meanY_BB=1.171, refSNP=rs145985409, zthresh_X=0.19811140407, zthresh_Y=0.172079887333} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0.01, GTA=0/0, GTZ=0/0, IGC=0.441, LRR=0.077, NORMX=1.276, NORMY=0.087, R=1.363, THETA=0.043, X=22154, Y=590}]] filters=
14:32:36.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.901, ILLUMINA_BUILD=37.2, ILLUMINA_CHR=3, ILLUMINA_POS=178962380, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1251, PROBE_A=CGACTGGCTGGACTGTGCCTTCACCTGTGGTGTGCACTGCCACGGTCAGG, PROBE_B=., SOURCE=1000genomes, devR_AA=0.1, devR_AB=0.133, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.009, devX_AA=0.101, devX_AB=0.054, devX_BB=0.013, devY_AA=0.032, devY_AB=0.054, devY_BB=0.097, meanR_AA=0.964, meanR_AB=1.179, meanR_BB=0.948, meanTHETA_AA=0.024, meanTHETA_AB=0.5, meanTHETA_BB=0.976, meanX_AA=0.928, meanX_AB=0.589, meanX_BB=0.034, meanY_AA=0.036, meanY_AB=0.59, meanY_BB=0.915, refSNP=rs199686819, zthresh_X=0.12173904259, zthresh_Y=0.159179424244} GT=[[0816201804HC0_R01C01 C*/C* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.508, LRR=-0.062, NORMX=0.033, NORMY=0.876, R=0.909, THETA=0.976, X=819, Y=4947}]] filters=
14:32:36.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 Q. of type=SNP alleles=[C*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=816, GC_SCORE=0.879, ILLUMINA_BUILD=37, ILLUMINA_CHR=3, ILLUMINA_POS=178962425, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=GAGAGAAGAATCGACCTGCACTGCCATCCACACAGATATCATGGACGACT, PROBE_B=., SOURCE=STAARS, devR_AA=0.1, devR_AB=0.121, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.011, devX_AA=0.101, devX_AB=0.054, devX_BB=0.014, devY_AA=0.029, devY_AB=0.053, devY_BB=0.095, meanR_AA=0.883, meanR_AB=1.074, meanR_BB=0.877, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.851, meanX_AB=0.543, meanX_BB=0.048, meanY_AA=0.032, meanY_AB=0.532, meanY_BB=0.829, refSNP=rs145138176, zthresh_X=0.14237441016, zthresh_Y=0.168724424863} GT=[[0816201804HC0_R01C01 C*/C* {BAF=0.999, GTA=0/0, GTZ=0/0, IGC=0.48, LRR=-0.121, NORMX=0.045, NORMY=0.761, R=0.806, THETA=0.963, X=1125, Y=4047}]] filters=
14:32:36.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968543 Q. of type=SNP alleles=[G*, T] attr={AC=0, AF=0.00, ALLELE_A=T, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.906, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968543, ILLUMINA_STRAND=TOP, N_AA=0, N_AB=1, N_BB=1250, PROBE_A=GGGCTTCTCAGTCCTAATGTTCTTCTTGCTCGGAACAACCATTCTAAAGC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.104, devR_AB=0.156, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.008, devX_AA=0.107, devX_AB=0.058, devX_BB=0.014, devY_AA=0.036, devY_AB=0.057, devY_BB=0.097, meanR_AA=1.1, meanR_AB=1.381, meanR_BB=1.127, meanTHETA_AA=0.025, meanTHETA_AB=0.492, meanTHETA_BB=0.975, meanX_AA=1.059, meanX_AB=0.7, meanX_BB=0.042, meanY_AA=0.041, meanY_AB=0.682, meanY_BB=1.085, refSNP=rs61734056, zthresh_X=0.135160960006, zthresh_Y=0.165299195841} GT=[[0816201804HC0_R01C01 G*/G* {BAF=1, GTA=0/0, GTZ=0/0, IGC=0.897, LRR=0.034, NORMX=0.04, NORMY=1.113, R=1.153, THETA=0.977, X=972, Y=6285}]] filters=
14:32:36.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968568 Q. of type=SNP alleles=[A*, C] attr={AC=0, AF=0.00, ALLELE_A=A*, ALLELE_B=C, AN=2, BEADSET_ID=1168, GC_SCORE=0.889, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968568, ILLUMINA_STRAND=BOT, N_AA=1249, N_AB=1, N_BB=0, PROBE_A=CCGTGATGCTGGGGTTTGCCATGATGGGCTTCTCAGTCCTAATGTTCTTC, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.143, devR_AB=0.175, devR_BB=0.109, devTHETA_AA=0.01, devTHETA_AB=0.022, devTHETA_BB=0.022, devX_AA=0.14, devX_AB=0.076, devX_BB=0.041, devY_AA=0.016, devY_AB=0.077, devY_BB=0.113, meanR_AA=1.113, meanR_AB=1.547, meanR_BB=1.25, meanTHETA_AA=0.019, meanTHETA_AB=0.509, meanTHETA_BB=0.975, meanX_AA=1.081, meanX_AB=0.763, meanX_BB=0.046, meanY_AA=0.032, meanY_AB=0.784, meanY_BB=1.204, refSNP=rs2276802, zthresh_X=0.189602852188, zthresh_Y=0.145988814983} GT=[[0816201804HC0_R01C01 A*/A* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.878, LRR=-0.023, NORMX=1.069, NORMY=0.021, R=1.089, THETA=0.012, X=17958, Y=362}]] filters=
14:32:36.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968634 Q. of type=SNP alleles=[C*, T] attr={AC=1, AF=0.500, ALLELE_A=T, ALLELE_B=C*, AN=2, BEADSET_ID=850, GC_SCORE=0.885, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968634, ILLUMINA_STRAND=TOP, N_AA=216, N_AB=596, N_BB=439, PROBE_A=ACTACAGTGATGGAGACCCACTAGATGTGCACAAGAGGCTGCCATCCAGT, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.011, devTHETA_AB=0.025, devTHETA_BB=0.01, devX_AA=0.096, devX_AB=0.058, devX_BB=0.015, devY_AA=0.019, devY_AB=0.054, devY_BB=0.097, meanR_AA=1.156, meanR_AB=1.266, meanR_BB=0.992, meanTHETA_AA=0.036, meanTHETA_AB=0.47, meanTHETA_BB=0.972, meanX_AA=1.094, meanX_AB=0.662, meanX_BB=0.042, meanY_AA=0.062, meanY_AB=0.603, meanY_BB=0.951, refSNP=rs7645550, zthresh_X=0.139062088415, zthresh_Y=0.166539592425} GT=[[0816201804HC0_R01C01 C*/T {BAF=0.496, GTA=1/0, GTZ=1/0, IGC=0.922, LRR=-0.041, NORMX=0.647, NORMY=0.582, R=1.23, THETA=0.466, X=11372, Y=3338}]] filters=
14:32:36.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968660 Q. of type=SNP alleles=[T*, C] attr={AC=0, AF=0.00, ALLELE_A=T*, ALLELE_B=C, AN=2, BEADSET_ID=850, GC_SCORE=0.862, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968660, ILLUMINA_STRAND=TOP, N_AA=987, N_AB=246, N_BB=18, PROBE_A=TGCCTCAGGGAAGAAGAGAGAGACAGACTACAGTGATGGAGACCCACTAG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.01, devTHETA_AB=0.039, devTHETA_BB=0.016, devX_AA=0.096, devX_AB=0.061, devX_BB=0.022, devY_AA=0.015, devY_AB=0.061, devY_BB=0.098, meanR_AA=1.016, meanR_AB=1.151, meanR_BB=0.92, meanTHETA_AA=0.036, meanTHETA_AB=0.5, meanTHETA_BB=0.97, meanX_AA=0.962, meanX_AB=0.575, meanX_BB=0.041, meanY_AA=0.054, meanY_AB=0.576, meanY_BB=0.878, refSNP=rs1170672, zthresh_X=0.191295862566, zthresh_Y=0.153061435119} GT=[[0816201804HC0_R01C01 T*/T* {BAF=0, GTA=0/0, GTZ=0/0, IGC=0.899, LRR=0.047, NORMX=1.001, NORMY=0.046, R=1.048, THETA=0.029, X=17415, Y=341}]] filters=
14:32:36.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968848 Q. of type=SNP alleles=[G*, A] attr={AC=0, AF=0.00, ALLELE_A=A, ALLELE_B=G*, AN=2, BEADSET_ID=850, GC_SCORE=0.884, ILLUMINA_BUILD=37.1, ILLUMINA_CHR=3, ILLUMINA_POS=178968848, ILLUMINA_STRAND=BOT, N_AA=0, N_AB=0, N_BB=1250, PROBE_A=TATTTAGATGGACTTTTCACCAAGCTCTGAACTGGGATTTCATTTTGTTG, PROBE_B=., SOURCE=ExomeSNPs, devR_AA=0.1, devR_AB=0.1, devR_BB=0.1, devTHETA_AA=0.022, devTHETA_AB=0.022, devTHETA_BB=0.015, devX_AA=0.099, devX_AB=0.052, devX_BB=0.015, devY_AA=0.022, devY_AB=0.051, devY_BB=0.096, meanR_AA=0.662, meanR_AB=0.79, meanR_BB=0.676, meanTHETA_AA=0.024, meanTHETA_AB=0.494, meanTHETA_BB=0.963, meanX_AA=0.638, meanX_AB=0.399, meanX_BB=0.037, meanY_AA=0.024, meanY_AB=0.391, meanY_BB=0.639, refSNP=rs113011029, zthresh_X=0.138051204865, zthresh_Y=0.165472197716} GT=[[0816201804HC0_R01C01 G*/G* {BAF=0.988, GTA=0/0, GTZ=0/0, IGC=0.486, LRR=0.095, NORMX=0.051, NORMY=0.674, R=0.725, THETA=0.952, X=1106, Y=3811}]] filters=
14:32:36.427 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:32:36.427 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:32:36.427 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:32:36.427 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:36.519 INFO  Funcotator - ------------------------------------------------------------
14:32:36.519 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:36.519 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:36.519 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:36.519 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:36.519 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:36 PM GMT
14:32:36.519 INFO  Funcotator - ------------------------------------------------------------
14:32:36.519 INFO  Funcotator - ------------------------------------------------------------
14:32:36.519 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:36.519 INFO  Funcotator - Picard Version: 3.4.0
14:32:36.519 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:36.519 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:36.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:36.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:36.519 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:36.519 INFO  Funcotator - Deflater: IntelDeflater
14:32:36.519 INFO  Funcotator - Inflater: IntelInflater
14:32:36.519 INFO  Funcotator - GCS max retries/reopens: 20
14:32:36.519 INFO  Funcotator - Requester pays: disabled
14:32:36.519 INFO  Funcotator - Initializing engine
14:32:36.520 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
14:32:36.521 INFO  Funcotator - Done initializing engine
14:32:36.521 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:36.521 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:36.521 INFO  Funcotator - Initializing data sources...
14:32:36.521 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:32:36.521 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:36.522 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.522 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.522 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.522 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:36.522 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:32:36.522 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.523 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
14:32:36.550 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.550 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:32:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:32:36.551 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.551 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:36.551 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.552 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.553 INFO  Funcotator - Initializing Funcotator Engine...
14:32:36.553 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:32:36.553 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:32:36.553 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8230881786856611374.vcf
14:32:36.556 INFO  ProgressMeter - Starting traversal
14:32:36.556 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:36.560 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
14:32:36.560 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:32:36.560 WARN  Funcotator - ================================================================================
14:32:36.560 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:32:36.560 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:32:36.560 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:32:36.560 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:32:36.560 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:32:36.560 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:32:36.560 WARN  Funcotator - --------------------------------------------------------------------------------
14:32:36.560 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:32:36.560 WARN  Funcotator -  run was misconfigured.     
14:32:36.560 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:32:36.560 WARN  Funcotator - ================================================================================
14:32:36.560 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:36.561 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8230881786856611374.vcf
14:32:36.653 INFO  Funcotator - ------------------------------------------------------------
14:32:36.654 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:32:36.654 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:32:36.654 INFO  Funcotator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:32:36.654 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:32:36.654 INFO  Funcotator - Start Date/Time: June 2, 2025 at 2:32:36 PM GMT
14:32:36.654 INFO  Funcotator - ------------------------------------------------------------
14:32:36.654 INFO  Funcotator - ------------------------------------------------------------
14:32:36.654 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:32:36.654 INFO  Funcotator - Picard Version: 3.4.0
14:32:36.654 INFO  Funcotator - Built for Spark Version: 3.5.0
14:32:36.654 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:32:36.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:32:36.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:32:36.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:32:36.654 INFO  Funcotator - Deflater: IntelDeflater
14:32:36.654 INFO  Funcotator - Inflater: IntelInflater
14:32:36.654 INFO  Funcotator - GCS max retries/reopens: 20
14:32:36.654 INFO  Funcotator - Requester pays: disabled
14:32:36.654 INFO  Funcotator - Initializing engine
14:32:36.655 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
14:32:36.656 INFO  Funcotator - Done initializing engine
14:32:36.656 INFO  Funcotator - Skipping sequence dictionary validation.
14:32:36.656 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:32:36.656 INFO  Funcotator - Initializing data sources...
14:32:36.656 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:32:36.656 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:32:36.656 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.657 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.657 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.657 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:32:36.657 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:32:36.657 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.658 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
14:32:36.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
14:32:36.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-06-02 14:32:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:32:36.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.702 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:32:36.703 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:32:36.703 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
14:32:36.704 INFO  Funcotator - Initializing Funcotator Engine...
14:32:36.704 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:32:36.704 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:32:36.704 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4258876098749249049.vcf
14:32:36.709 INFO  ProgressMeter - Starting traversal
14:32:36.709 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:32:36.712 INFO  ProgressMeter -             unmapped              0.0                     1          20000.0
14:32:36.712 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:32:36.712 WARN  Funcotator - ================================================================================
14:32:36.712 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:32:36.712 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:32:36.712 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:32:36.712 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:32:36.712 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:32:36.712 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:32:36.712 WARN  Funcotator - --------------------------------------------------------------------------------
14:32:36.712 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:32:36.712 WARN  Funcotator -  run was misconfigured.     
14:32:36.712 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:32:36.712 WARN  Funcotator - ================================================================================
14:32:36.713 INFO  Funcotator - Shutting down engine
[June 2, 2025 at 2:32:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3244294144
14:32:36.714 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4258876098749249049.vcf