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

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

tests
0

failures
0

ignored
1m43.81s

duration
100%

successful

Tests

Test Duration Result
exhaustiveArgumentTest[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.128s passed
exhaustiveArgumentTest[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.170s passed
exhaustiveArgumentTest[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 0.968s passed
exhaustiveArgumentTest[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.050s passed
exhaustiveArgumentTest[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.010s passed
exhaustiveArgumentTest[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.037s passed
exhaustiveArgumentTest[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.022s passed
exhaustiveArgumentTest[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.065s 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) 6.326s 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) 5.635s 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) 2.139s 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) 1.987s 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) 12.880s 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) 5.998s 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 0.220s passed
testCanAnnotateMixedContigHg19Clinvar 0.134s passed
testCanAnnotateSpanningDeletions 0.231s passed
testCanCreateNonLocatableFuncotations 1.014s passed
testCanHandleSymbollicAlleleFuncotations 1.083s passed
testCustomVariantClassificationOrder 1.130s passed
testEColiFuncotations 0.127s passed
testEnsureDbSnpInMaf 0.143s passed
testExclusionFromDatasourceVcfToVcf 0.205s passed
testFilterParsing 0.145s passed
testFuncotatorWithoutValidatingResults[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.054s passed
testFuncotatorWithoutValidatingResults[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.210s passed
testFuncotatorWithoutValidatingResults[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 1.042s passed
testFuncotatorWithoutValidatingResults[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.128s passed
testFuncotatorWithoutValidatingResults[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.017s passed
testFuncotatorWithoutValidatingResults[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.118s passed
testFuncotatorWithoutValidatingResults[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder3310164094889814484/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.051s passed
testFuncotatorWithoutValidatingResults[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.176s passed
testMANESelectAnnotationDifferencesAndGencodeV43 0.462s passed
testMafCustomCountFieldsTumorOnly[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf) 0.117s passed
testMafCustomCountFieldsTumorOnly[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf) 0.113s passed
testMafCustomCountFields[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf) 0.111s passed
testMafCustomCountFields[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf) 0.110s passed
testManualAnnotationsCorrectness 0.123s passed
testMoreThanOneTNPair 0.107s passed
testNoSpanningDeletionWriteWithMAF 0.157s passed
testNoVariantsProduceMaf 0.102s 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) 5.927s passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput 0.902s passed
testVCFColumnsArentShuffled 0.109s passed
testVCFToMAFPreservesFields 0.117s passed
testVCFToVCFPreservesFields 0.121s passed
testVcfDatasourceAccountsForAltAlleles 0.150s passed
testVcfMafConcordance[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder8948850981284277312/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15) 0.233s passed
testVcfMafConcordance[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder8948850981284277312/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.316s passed
testVcfMafConcordance[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder2812458456308181539/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057) 36.554s passed
testVcfMafConcordance[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder15349367684819666215/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) 0.444s passed
testVcfMafConcordance[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder8948850981284277312/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) 0.301s passed
testVcfToMafHonorsExcludedFields 0.120s passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified 0.140s passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations 0.133s passed

Standard error

13:59:59.679 INFO  Funcotator - ------------------------------------------------------------
13:59:59.679 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
13:59:59.679 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:59:59.679 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
13:59:59.679 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
13:59:59.679 INFO  Funcotator - Start Date/Time: May 27, 2025 at 1:59:59 PM GMT
13:59:59.679 INFO  Funcotator - ------------------------------------------------------------
13:59:59.679 INFO  Funcotator - ------------------------------------------------------------
13:59:59.680 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
13:59:59.680 INFO  Funcotator - Picard Version: 3.4.0
13:59:59.680 INFO  Funcotator - Built for Spark Version: 3.5.0
13:59:59.680 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:59:59.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:59:59.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:59:59.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:59:59.680 INFO  Funcotator - Deflater: IntelDeflater
13:59:59.680 INFO  Funcotator - Inflater: IntelInflater
13:59:59.680 INFO  Funcotator - GCS max retries/reopens: 20
13:59:59.680 INFO  Funcotator - Requester pays: disabled
13:59:59.680 INFO  Funcotator - Initializing engine
13:59:59.681 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
13:59:59.682 INFO  Funcotator - Done initializing engine
13:59:59.682 INFO  Funcotator - Skipping sequence dictionary validation.
13:59:59.682 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:59:59.682 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder16848573455124719078/TranscriptIdFile.txt
13:59:59.682 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
13:59:59.682 INFO  FuncotatorEngine - Transcript parsing complete.
13:59:59.682 INFO  Funcotator - Initializing data sources...
13:59:59.682 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
13:59:59.683 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
13:59:59.683 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
13:59:59.683 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
13:59:59.684 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
13:59:59.684 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
13:59:59.684 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
13:59:59.684 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
13:59:59.684 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
13:59:59.685 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
13:59:59.685 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
13:59:59.685 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
13:59:59.685 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
13:59:59.686 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
13:59:59.686 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
13:59:59.686 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
13:59:59.686 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
13:59:59.686 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:59:59.686 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
13:59:59.687 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
13:59:59.709 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
13:59:59.710 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
13:59:59.755 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
13:59:59.756 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
14:00:00.345 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
14:00:00.345 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:00.347 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:00.349 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
14:00:00.352 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:00.355 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:00.355 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
14:00:00.356 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:00.395 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
14:00:00.395 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	2025-05-27 14:00:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:00.396 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
14:00:00.434 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
14:00:00.434 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
14:00:00.434 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
14:00:00.442 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:00.516 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
14:00:00.516 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:00.517 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:00.517 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
14:00:00.616 INFO  Funcotator - Initializing Funcotator Engine...
14:00:00.616 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
14:00:00.617 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:00.617 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:00.617 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:00.617 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:00.618 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:00.619 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:00.620 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:00.620 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:00.620 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:00.620 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.34851873946845246892.vcf
14:00:00.620 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
14:00:00.624 INFO  ProgressMeter - Starting traversal
14:00:00.624 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:00.701 INFO  ProgressMeter -             unmapped              0.0                     3           2337.7
14:00:00.701 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:00.701 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:00.705 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:00.810 INFO  Funcotator - ------------------------------------------------------------
14:00:00.810 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:00.810 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:00.810 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:00.810 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:00.810 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:00 PM GMT
14:00:00.810 INFO  Funcotator - ------------------------------------------------------------
14:00:00.810 INFO  Funcotator - ------------------------------------------------------------
14:00:00.810 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:00.810 INFO  Funcotator - Picard Version: 3.4.0
14:00:00.810 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:00.810 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:00.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:00.811 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:00.811 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:00.811 INFO  Funcotator - Deflater: IntelDeflater
14:00:00.811 INFO  Funcotator - Inflater: IntelInflater
14:00:00.811 INFO  Funcotator - GCS max retries/reopens: 20
14:00:00.811 INFO  Funcotator - Requester pays: disabled
14:00:00.811 INFO  Funcotator - Initializing engine
14:00:00.812 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:00.812 INFO  Funcotator - Done initializing engine
14:00:00.812 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:00.813 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:00.813 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13440489968538096947/TranscriptIdFile.txt
14:00:00.813 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:00:00.813 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:00.813 INFO  Funcotator - Initializing data sources...
14:00:00.813 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:00.813 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:00.813 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
14:00:00.814 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
14:00:00.814 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
14:00:00.814 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
14:00:00.814 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
14:00:00.815 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
14:00:00.815 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
14:00:00.815 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
14:00:00.815 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
14:00:00.816 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
14:00:00.816 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
14:00:00.816 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
14:00:00.816 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:00.817 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
14:00:00.817 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
14:00:00.817 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:00.817 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
14:00:00.817 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
14:00:00.847 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
14:00:00.848 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
14:00:00.895 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
14:00:00.896 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
14:00:01.457 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
14:00:01.458 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:01.459 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:01.461 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
14:00:01.464 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:01.467 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:01.467 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
14:00:01.468 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:01.499 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
14:00:01.499 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	2025-05-27 14:00:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:01.500 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
14:00:01.538 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
14:00:01.538 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
14:00:01.538 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
14:00:01.546 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:01.546 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
14:00:01.546 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:01.547 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:01.548 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
14:00:01.637 INFO  Funcotator - Initializing Funcotator Engine...
14:00:01.637 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:01.637 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:01.637 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.49484485622305763455.vcf
14:00:01.639 INFO  ProgressMeter - Starting traversal
14:00:01.639 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:01.874 INFO  ProgressMeter -             unmapped              0.0                     4           1021.3
14:00:01.874 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:01.874 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:01.875 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:01.973 INFO  Funcotator - ------------------------------------------------------------
14:00:01.973 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:01.973 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:01.973 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:01.973 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:01.973 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:01 PM GMT
14:00:01.973 INFO  Funcotator - ------------------------------------------------------------
14:00:01.973 INFO  Funcotator - ------------------------------------------------------------
14:00:01.973 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:01.973 INFO  Funcotator - Picard Version: 3.4.0
14:00:01.973 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:01.973 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:01.973 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:01.973 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:01.973 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:01.973 INFO  Funcotator - Deflater: IntelDeflater
14:00:01.973 INFO  Funcotator - Inflater: IntelInflater
14:00:01.973 INFO  Funcotator - GCS max retries/reopens: 20
14:00:01.973 INFO  Funcotator - Requester pays: disabled
14:00:01.974 INFO  Funcotator - Initializing engine
14:00:01.975 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:01.976 INFO  Funcotator - Done initializing engine
14:00:01.976 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:01.976 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:01.976 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder12500615898477171227/TranscriptIdFile.txt
14:00:01.976 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:00:01.976 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:01.976 INFO  Funcotator - Initializing data sources...
14:00:01.976 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:01.976 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:01.977 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
14:00:01.977 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
14:00:01.977 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
14:00:01.977 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
14:00:01.978 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
14:00:01.978 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
14:00:01.978 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
14:00:01.978 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
14:00:01.978 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
14:00:01.979 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
14:00:01.979 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
14:00:01.979 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
14:00:01.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:01.980 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
14:00:01.980 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
14:00:01.980 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:01.980 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
14:00:01.980 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
14:00:02.000 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
14:00:02.001 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
14:00:02.049 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
14:00:02.049 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
14:00:02.637 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
14:00:02.637 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:02.638 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:02.640 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
14:00:02.643 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:02.645 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:02.645 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
14:00:02.646 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:02.673 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
14:00:02.673 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	2025-05-27 14:00:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:02.674 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
14:00:02.713 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
14:00:02.713 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
14:00:02.713 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
14:00:02.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:02.721 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
14:00:02.721 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:02.722 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:02.722 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
14:00:02.811 INFO  Funcotator - Initializing Funcotator Engine...
14:00:02.811 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
14:00:02.811 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:02.811 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:02.811 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:02.811 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:02.812 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:02.813 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:02.813 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:02.813 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.39789073978528021802.vcf
14:00:02.814 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
14:00:02.815 INFO  ProgressMeter - Starting traversal
14:00:02.815 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:02.840 INFO  ProgressMeter -             unmapped              0.0                     3           7200.0
14:00:02.840 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:02.840 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:02.842 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:02 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2772434944
14:00:02.940 INFO  Funcotator - ------------------------------------------------------------
14:00:02.940 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:02.940 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:02.940 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:02.940 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:02.940 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:02 PM GMT
14:00:02.940 INFO  Funcotator - ------------------------------------------------------------
14:00:02.940 INFO  Funcotator - ------------------------------------------------------------
14:00:02.940 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:02.940 INFO  Funcotator - Picard Version: 3.4.0
14:00:02.940 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:02.940 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:02.940 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:02.940 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:02.940 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:02.940 INFO  Funcotator - Deflater: IntelDeflater
14:00:02.940 INFO  Funcotator - Inflater: IntelInflater
14:00:02.940 INFO  Funcotator - GCS max retries/reopens: 20
14:00:02.940 INFO  Funcotator - Requester pays: disabled
14:00:02.940 INFO  Funcotator - Initializing engine
14:00:02.941 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:02.942 INFO  Funcotator - Done initializing engine
14:00:02.942 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:02.942 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:02.942 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2771056365512598017/TranscriptIdFile.txt
14:00:02.942 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:00:02.942 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:02.942 INFO  Funcotator - Initializing data sources...
14:00:02.942 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:02.942 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:02.943 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
14:00:02.943 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
14:00:02.943 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
14:00:02.943 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
14:00:02.943 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
14:00:02.944 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
14:00:02.944 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
14:00:02.944 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
14:00:02.944 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
14:00:02.944 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
14:00:02.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
14:00:02.945 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
14:00:02.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:02.945 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
14:00:02.945 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
14:00:02.945 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:02.945 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
14:00:02.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
14:00:02.967 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
14:00:02.967 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
14:00:03.014 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
14:00:03.015 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
14:00:03.597 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
14:00:03.597 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:03.598 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:03.600 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
14:00:03.603 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:03.606 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:03.607 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
14:00:03.608 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:03.636 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
14:00:03.636 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	2025-05-27 14:00:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:03.636 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
14:00:03.674 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
14:00:03.674 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
14:00:03.675 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
14:00:03.682 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:03.682 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
14:00:03.682 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:03.683 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:03.684 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
14:00:03.771 INFO  Funcotator - Initializing Funcotator Engine...
14:00:03.771 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:03.771 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:03.771 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.418144373799608092568.vcf
14:00:03.772 INFO  ProgressMeter - Starting traversal
14:00:03.772 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:03.892 INFO  ProgressMeter -             unmapped              0.0                     4           2000.0
14:00:03.892 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:03.892 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:03.893 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:03 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:03.987 INFO  Funcotator - ------------------------------------------------------------
14:00:03.987 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:03.987 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:03.987 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:03.987 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:03.987 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:03 PM GMT
14:00:03.987 INFO  Funcotator - ------------------------------------------------------------
14:00:03.987 INFO  Funcotator - ------------------------------------------------------------
14:00:03.987 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:03.987 INFO  Funcotator - Picard Version: 3.4.0
14:00:03.987 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:03.987 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:03.987 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:03.987 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:03.987 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:03.987 INFO  Funcotator - Deflater: IntelDeflater
14:00:03.987 INFO  Funcotator - Inflater: IntelInflater
14:00:03.987 INFO  Funcotator - GCS max retries/reopens: 20
14:00:03.987 INFO  Funcotator - Requester pays: disabled
14:00:03.987 INFO  Funcotator - Initializing engine
14:00:03.988 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:03.989 INFO  Funcotator - Done initializing engine
14:00:03.989 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:03.989 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:03.989 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8984830047008952744/TranscriptIdFile.txt
14:00:03.989 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:00:03.989 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:03.989 INFO  Funcotator - Initializing data sources...
14:00:03.989 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:03.989 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:03.990 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
14:00:03.990 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
14:00:03.990 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
14:00:03.990 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
14:00:03.990 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
14:00:03.991 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
14:00:03.991 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
14:00:03.991 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
14:00:03.991 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
14:00:03.991 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
14:00:03.992 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
14:00:03.992 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
14:00:03.992 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:03.992 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
14:00:03.992 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
14:00:03.992 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:03.992 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
14:00:03.993 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
14:00:04.012 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
14:00:04.013 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
14:00:04.083 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
14:00:04.083 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
14:00:04.632 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
14:00:04.632 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:04.633 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:04.635 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
14:00:04.638 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:04.640 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:04.640 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
14:00:04.641 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:04.668 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
14:00:04.668 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	2025-05-27 14:00:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:04.668 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
14:00:04.707 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
14:00:04.707 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
14:00:04.707 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
14:00:04.715 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:04.715 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
14:00:04.715 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:04.716 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:04.716 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
14:00:04.866 INFO  Funcotator - Initializing Funcotator Engine...
14:00:04.866 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
14:00:04.866 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:04.866 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:04.866 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:04.866 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:04.866 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:04.866 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:04.866 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:04.867 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:04.867 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:04.867 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.316932337080214854939.maf
14:00:04.869 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
14:00:04.871 INFO  ProgressMeter - Starting traversal
14:00:04.871 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:04.902 INFO  ProgressMeter -             unmapped              0.0                     3           5806.5
14:00:04.903 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:04.903 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:04.903 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:04.998 INFO  Funcotator - ------------------------------------------------------------
14:00:04.998 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:04.998 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:04.998 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:04.998 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:04.999 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:04 PM GMT
14:00:04.999 INFO  Funcotator - ------------------------------------------------------------
14:00:04.999 INFO  Funcotator - ------------------------------------------------------------
14:00:04.999 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:04.999 INFO  Funcotator - Picard Version: 3.4.0
14:00:04.999 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:04.999 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:04.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:04.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:04.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:04.999 INFO  Funcotator - Deflater: IntelDeflater
14:00:04.999 INFO  Funcotator - Inflater: IntelInflater
14:00:04.999 INFO  Funcotator - GCS max retries/reopens: 20
14:00:04.999 INFO  Funcotator - Requester pays: disabled
14:00:04.999 INFO  Funcotator - Initializing engine
14:00:05.000 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:05.000 INFO  Funcotator - Done initializing engine
14:00:05.000 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:05.000 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:05.000 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder10689092605750096195/TranscriptIdFile.txt
14:00:05.000 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:00:05.000 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:05.000 INFO  Funcotator - Initializing data sources...
14:00:05.000 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:05.001 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:05.001 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
14:00:05.001 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
14:00:05.001 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
14:00:05.002 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
14:00:05.002 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
14:00:05.002 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
14:00:05.002 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
14:00:05.002 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
14:00:05.003 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
14:00:05.003 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
14:00:05.003 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
14:00:05.003 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
14:00:05.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:05.003 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
14:00:05.004 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
14:00:05.004 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:05.004 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
14:00:05.004 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
14:00:05.025 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
14:00:05.025 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
14:00:05.074 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
14:00:05.074 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
14:00:05.656 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
14:00:05.656 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:05.658 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:05.660 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
14:00:05.663 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:05.665 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:05.665 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
14:00:05.665 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:05.693 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
14:00:05.693 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	2025-05-27 14:00:05	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:05.693 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
14:00:05.732 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
14:00:05.732 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
14:00:05.733 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
14:00:05.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:05.740 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
14:00:05.740 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:05.741 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:05.742 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
14:00:05.826 INFO  Funcotator - Initializing Funcotator Engine...
14:00:05.826 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:05.826 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:05.826 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.416690804465275174385.maf
14:00:05.827 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:00:05.828 INFO  ProgressMeter - Starting traversal
14:00:05.828 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:05.940 INFO  ProgressMeter -             unmapped              0.0                     4           2162.2
14:00:05.940 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:05.940 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:05.940 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:06.033 INFO  Funcotator - ------------------------------------------------------------
14:00:06.033 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:06.033 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:06.033 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:06.033 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:06.033 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:06 PM GMT
14:00:06.033 INFO  Funcotator - ------------------------------------------------------------
14:00:06.033 INFO  Funcotator - ------------------------------------------------------------
14:00:06.034 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:06.034 INFO  Funcotator - Picard Version: 3.4.0
14:00:06.034 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:06.034 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:06.034 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:06.034 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:06.034 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:06.034 INFO  Funcotator - Deflater: IntelDeflater
14:00:06.034 INFO  Funcotator - Inflater: IntelInflater
14:00:06.034 INFO  Funcotator - GCS max retries/reopens: 20
14:00:06.034 INFO  Funcotator - Requester pays: disabled
14:00:06.034 INFO  Funcotator - Initializing engine
14:00:06.035 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:06.036 INFO  Funcotator - Done initializing engine
14:00:06.036 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:06.036 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:06.036 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2051833945389861070/TranscriptIdFile.txt
14:00:06.036 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
14:00:06.036 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:06.036 INFO  Funcotator - Initializing data sources...
14:00:06.036 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:06.036 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:06.036 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
14:00:06.037 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
14:00:06.037 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
14:00:06.037 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
14:00:06.037 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
14:00:06.038 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
14:00:06.038 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
14:00:06.038 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
14:00:06.038 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
14:00:06.038 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
14:00:06.039 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
14:00:06.039 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
14:00:06.039 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:06.039 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
14:00:06.039 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
14:00:06.039 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:06.039 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
14:00:06.040 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
14:00:06.060 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
14:00:06.060 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
14:00:06.108 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
14:00:06.109 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
14:00:06.700 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
14:00:06.700 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:06.701 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:06.703 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
14:00:06.706 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:06.708 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:06.708 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
14:00:06.708 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:06.736 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
14:00:06.736 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	2025-05-27 14:00:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:06.736 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
14:00:06.774 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
14:00:06.774 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
14:00:06.775 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
14:00:06.782 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:06.782 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
14:00:06.782 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:06.783 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:06.784 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
14:00:06.869 INFO  Funcotator - Initializing Funcotator Engine...
14:00:06.869 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
14:00:06.869 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:06.869 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:06.869 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:06.869 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:06.870 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:06.870 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:06.870 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.34946417579913764049.maf
14:00:06.870 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
14:00:06.872 INFO  ProgressMeter - Starting traversal
14:00:06.872 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:06.962 INFO  ProgressMeter -             unmapped              0.0                     3           2000.0
14:00:06.962 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:06.962 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:06.962 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:06 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:07.060 INFO  Funcotator - ------------------------------------------------------------
14:00:07.060 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:07.060 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:07.060 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:07.060 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:07.060 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:07 PM GMT
14:00:07.060 INFO  Funcotator - ------------------------------------------------------------
14:00:07.060 INFO  Funcotator - ------------------------------------------------------------
14:00:07.060 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:07.060 INFO  Funcotator - Picard Version: 3.4.0
14:00:07.060 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:07.060 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:07.060 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:07.060 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:07.060 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:07.060 INFO  Funcotator - Deflater: IntelDeflater
14:00:07.060 INFO  Funcotator - Inflater: IntelInflater
14:00:07.060 INFO  Funcotator - GCS max retries/reopens: 20
14:00:07.060 INFO  Funcotator - Requester pays: disabled
14:00:07.060 INFO  Funcotator - Initializing engine
14:00:07.061 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:07.062 INFO  Funcotator - Done initializing engine
14:00:07.062 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:07.062 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:07.062 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2117551990722173001/TranscriptIdFile.txt
14:00:07.062 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
14:00:07.062 INFO  FuncotatorEngine - Transcript parsing complete.
14:00:07.062 INFO  Funcotator - Initializing data sources...
14:00:07.062 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:07.062 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:07.062 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
14:00:07.062 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
14:00:07.063 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
14:00:07.063 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
14:00:07.063 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
14:00:07.063 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
14:00:07.063 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
14:00:07.064 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
14:00:07.064 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
14:00:07.064 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
14:00:07.064 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
14:00:07.064 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
14:00:07.065 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:07.065 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
14:00:07.065 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
14:00:07.065 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:07.065 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
14:00:07.065 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
14:00:07.086 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
14:00:07.087 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
14:00:07.133 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
14:00:07.134 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
14:00:07.747 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
14:00:07.747 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:07.748 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:07.750 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
14:00:07.753 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:07.755 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:07.755 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
14:00:07.756 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:07.783 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
14:00:07.783 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	2025-05-27 14:00:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:07.783 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
14:00:07.821 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
14:00:07.821 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
14:00:07.822 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
14:00:07.829 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:07.830 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
14:00:07.830 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:07.831 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:07.831 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
14:00:07.911 INFO  Funcotator - Initializing Funcotator Engine...
14:00:07.911 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:07.911 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:07.911 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.417745434082481895397.maf
14:00:07.911 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
14:00:07.913 INFO  ProgressMeter - Starting traversal
14:00:07.913 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:08.027 INFO  ProgressMeter -             unmapped              0.0                     4           2105.3
14:00:08.027 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:08.027 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:08.027 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:08 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2772434944
14:00:08.127 INFO  Funcotator - ------------------------------------------------------------
14:00:08.127 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:08.127 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:08.127 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:08.127 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:08.127 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:08 PM GMT
14:00:08.127 INFO  Funcotator - ------------------------------------------------------------
14:00:08.127 INFO  Funcotator - ------------------------------------------------------------
14:00:08.127 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:08.127 INFO  Funcotator - Picard Version: 3.4.0
14:00:08.127 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:08.127 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:08.127 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:08.127 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:08.127 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:08.127 INFO  Funcotator - Deflater: IntelDeflater
14:00:08.127 INFO  Funcotator - Inflater: IntelInflater
14:00:08.127 INFO  Funcotator - GCS max retries/reopens: 20
14:00:08.127 INFO  Funcotator - Requester pays: disabled
14:00:08.127 INFO  Funcotator - Initializing engine
14:00:08.130 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:00:08.138 INFO  Funcotator - Done initializing engine
14:00:08.138 INFO  Funcotator - Validating sequence dictionaries...
14:00:08.138 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:08.138 INFO  Funcotator - Initializing data sources...
14:00:08.138 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:08.138 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:08.139 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
14:00:08.139 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
14:00:08.139 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
14:00:08.139 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
14:00:08.140 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
14:00:08.140 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
14:00:08.140 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
14:00:08.140 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
14:00:08.140 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
14:00:08.141 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
14:00:08.141 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
14:00:08.141 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
14:00:08.141 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:08.141 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
14:00:08.141 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
14:00:08.141 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:08.142 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
14:00:08.142 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
14:00:08.162 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
14:00:08.162 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
14:00:08.208 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
14:00:08.209 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
14:00:08.799 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
14:00:08.799 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:08.800 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:08.802 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
14:00:08.804 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:08.806 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:08.807 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
14:00:08.807 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:08.834 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
14:00:08.834 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	2025-05-27 14:00:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:08.835 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
14:00:08.874 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
14:00:08.874 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
14:00:08.874 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
14:00:08.882 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:08.883 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
14:00:08.883 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:08.883 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:08.884 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
14:00:08.964 INFO  Funcotator - Initializing Funcotator Engine...
14:00:08.964 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:08.964 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.
14:00:08.964 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator9421403867026127045.vcf
14:00:08.965 INFO  ProgressMeter - Starting traversal
14:00:08.965 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:11.264 INFO  ProgressMeter -             unmapped              0.0                   198           5167.5
14:00:11.264 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:00:11.264 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:00:11.272 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:11 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2810183680
14:00:11.273 WARN  gatk -   VCF Elapsed Time: 3.244337363s
14:00:11.274 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator9421403867026127045.vcf
14:00:11.277 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:00:11.397 INFO  Funcotator - ------------------------------------------------------------
14:00:11.397 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:11.397 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:11.397 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:11.397 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:11.397 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:11 PM GMT
14:00:11.397 INFO  Funcotator - ------------------------------------------------------------
14:00:11.397 INFO  Funcotator - ------------------------------------------------------------
14:00:11.397 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:11.397 INFO  Funcotator - Picard Version: 3.4.0
14:00:11.397 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:11.397 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:11.397 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:11.397 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:11.397 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:11.397 INFO  Funcotator - Deflater: IntelDeflater
14:00:11.397 INFO  Funcotator - Inflater: IntelInflater
14:00:11.397 INFO  Funcotator - GCS max retries/reopens: 20
14:00:11.397 INFO  Funcotator - Requester pays: disabled
14:00:11.397 INFO  Funcotator - Initializing engine
14:00:11.399 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:00:11.400 INFO  Funcotator - Done initializing engine
14:00:11.400 INFO  Funcotator - Validating sequence dictionaries...
14:00:11.401 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:11.401 INFO  Funcotator - Initializing data sources...
14:00:11.401 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:11.401 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:11.401 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
14:00:11.401 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
14:00:11.402 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
14:00:11.402 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
14:00:11.402 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
14:00:11.402 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
14:00:11.402 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
14:00:11.403 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
14:00:11.403 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
14:00:11.403 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
14:00:11.403 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
14:00:11.404 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
14:00:11.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:11.404 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
14:00:11.404 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
14:00:11.404 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:11.404 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
14:00:11.405 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
14:00:11.432 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
14:00:11.433 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
14:00:11.479 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
14:00:11.480 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
14:00:12.072 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
14:00:12.072 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:12.073 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:12.075 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
14:00:12.078 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:12.080 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:12.081 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
14:00:12.081 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:12.108 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
14:00:12.108 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	2025-05-27 14:00:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:12.109 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
14:00:12.149 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
14:00:12.149 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
14:00:12.149 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
14:00:12.157 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:12.157 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
14:00:12.157 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:12.158 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:12.158 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
14:00:12.239 INFO  Funcotator - Initializing Funcotator Engine...
14:00:12.240 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:12.240 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.
14:00:12.240 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator9893769284804299074.maf
14:00:12.240 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
14:00:12.241 INFO  ProgressMeter - Starting traversal
14:00:12.241 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:14.351 INFO  ProgressMeter -             unmapped              0.0                   198           5630.3
14:00:14.351 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:00:14.351 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:00:14.351 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:14 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2810183680
14:00:14.352 WARN  gatk -   MAF Elapsed Time: 3.070937205s
14:00:14.448 INFO  Funcotator - ------------------------------------------------------------
14:00:14.449 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:14.449 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:14.449 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:14.449 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:14.449 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:14 PM GMT
14:00:14.449 INFO  Funcotator - ------------------------------------------------------------
14:00:14.449 INFO  Funcotator - ------------------------------------------------------------
14:00:14.449 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:14.449 INFO  Funcotator - Picard Version: 3.4.0
14:00:14.449 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:14.449 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:14.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:14.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:14.449 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:14.449 INFO  Funcotator - Deflater: IntelDeflater
14:00:14.449 INFO  Funcotator - Inflater: IntelInflater
14:00:14.449 INFO  Funcotator - GCS max retries/reopens: 20
14:00:14.449 INFO  Funcotator - Requester pays: disabled
14:00:14.449 INFO  Funcotator - Initializing engine
14:00:14.451 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
14:00:14.452 INFO  Funcotator - Done initializing engine
14:00:14.452 INFO  Funcotator - Validating sequence dictionaries...
14:00:14.452 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:14.452 INFO  Funcotator - Initializing data sources...
14:00:14.452 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:14.452 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:14.453 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
14:00:14.453 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
14:00:14.453 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
14:00:14.453 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
14:00:14.453 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
14:00:14.454 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
14:00:14.454 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
14:00:14.454 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
14:00:14.454 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
14:00:14.454 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
14:00:14.454 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
14:00:14.455 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
14:00:14.455 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:14.455 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
14:00:14.455 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
14:00:14.455 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:14.455 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
14:00:14.456 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
14:00:14.476 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
14:00:14.477 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
14:00:14.523 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
14:00:14.524 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
14:00:15.137 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
14:00:15.137 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:15.138 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:15.140 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
14:00:15.143 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:15.145 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:15.146 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
14:00:15.146 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:15.173 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
14:00:15.174 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	2025-05-27 14:00:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:15.174 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
14:00:15.212 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
14:00:15.212 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
14:00:15.213 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
14:00:15.220 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:15.220 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
14:00:15.220 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:15.221 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:15.221 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
14:00:15.301 INFO  Funcotator - Initializing Funcotator Engine...
14:00:15.301 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:15.301 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.
14:00:15.301 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator13960918069858964721.vcf
14:00:15.303 INFO  ProgressMeter - Starting traversal
14:00:15.303 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:16.345 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:00:16.345 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:00:17.153 INFO  ProgressMeter -             unmapped              0.0                   168           5448.6
14:00:17.153 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:00:17.153 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:00:17.162 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2810183680
14:00:17.162 WARN  gatk -   VCF Elapsed Time: 2.807704174s
14:00:17.163 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator13960918069858964721.vcf
14:00:17.166 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
14:00:17.264 INFO  Funcotator - ------------------------------------------------------------
14:00:17.264 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:17.264 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:17.264 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:17.264 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:17.264 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:17 PM GMT
14:00:17.264 INFO  Funcotator - ------------------------------------------------------------
14:00:17.264 INFO  Funcotator - ------------------------------------------------------------
14:00:17.264 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:17.264 INFO  Funcotator - Picard Version: 3.4.0
14:00:17.264 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:17.264 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:17.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:17.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:17.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:17.264 INFO  Funcotator - Deflater: IntelDeflater
14:00:17.264 INFO  Funcotator - Inflater: IntelInflater
14:00:17.264 INFO  Funcotator - GCS max retries/reopens: 20
14:00:17.264 INFO  Funcotator - Requester pays: disabled
14:00:17.264 INFO  Funcotator - Initializing engine
14:00:17.266 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
14:00:17.267 INFO  Funcotator - Done initializing engine
14:00:17.267 INFO  Funcotator - Validating sequence dictionaries...
14:00:17.267 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:17.267 INFO  Funcotator - Initializing data sources...
14:00:17.267 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:17.267 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:17.268 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
14:00:17.268 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
14:00:17.268 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
14:00:17.268 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
14:00:17.269 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
14:00:17.269 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
14:00:17.269 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
14:00:17.269 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
14:00:17.269 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
14:00:17.270 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
14:00:17.270 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
14:00:17.270 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
14:00:17.270 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:17.270 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
14:00:17.270 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
14:00:17.270 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:17.270 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
14:00:17.271 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
14:00:17.291 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
14:00:17.291 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
14:00:17.337 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
14:00:17.338 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
14:00:17.942 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
14:00:17.942 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:17.943 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:17.945 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
14:00:17.948 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:17.950 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:17.950 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
14:00:17.951 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:17.991 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
14:00:17.991 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	2025-05-27 14:00:17	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:17.991 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
14:00:18.030 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
14:00:18.030 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
14:00:18.031 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
14:00:18.039 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:18.039 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
14:00:18.039 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:18.040 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:18.040 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
14:00:18.122 INFO  Funcotator - Initializing Funcotator Engine...
14:00:18.122 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:18.122 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.
14:00:18.122 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator14061789428904603429.maf
14:00:18.122 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
14:00:18.123 INFO  ProgressMeter - Starting traversal
14:00:18.123 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:19.188 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:00:19.188 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
14:00:19.987 INFO  ProgressMeter -             unmapped              0.0                   168           5407.7
14:00:19.987 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
14:00:19.987 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
14:00:19.987 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2845835264
14:00:19.987 WARN  gatk -   MAF Elapsed Time: 2.818325211s
14:00:20.090 INFO  Funcotator - ------------------------------------------------------------
14:00:20.090 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:20.090 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:20.090 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:20.090 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:20.090 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:20 PM GMT
14:00:20.090 INFO  Funcotator - ------------------------------------------------------------
14:00:20.090 INFO  Funcotator - ------------------------------------------------------------
14:00:20.090 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:20.090 INFO  Funcotator - Picard Version: 3.4.0
14:00:20.090 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:20.090 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:20.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:20.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:20.090 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:20.090 INFO  Funcotator - Deflater: IntelDeflater
14:00:20.090 INFO  Funcotator - Inflater: IntelInflater
14:00:20.090 INFO  Funcotator - GCS max retries/reopens: 20
14:00:20.090 INFO  Funcotator - Requester pays: disabled
14:00:20.090 INFO  Funcotator - Initializing engine
14:00:20.092 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
14:00:20.093 INFO  Funcotator - Done initializing engine
14:00:20.093 INFO  Funcotator - Validating sequence dictionaries...
14:00:20.093 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:20.093 INFO  Funcotator - Initializing data sources...
14:00:20.093 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:20.093 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:20.094 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
14:00:20.094 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
14:00:20.094 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
14:00:20.094 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
14:00:20.094 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
14:00:20.095 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
14:00:20.112 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
14:00:20.112 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
14:00:20.112 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
14:00:20.112 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
14:00:20.112 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
14:00:20.113 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
14:00:20.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:20.113 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
14:00:20.113 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
14:00:20.113 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:20.113 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
14:00:20.113 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
14:00:20.133 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
14:00:20.134 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
14:00:20.180 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
14:00:20.180 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
14:00:20.782 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
14:00:20.782 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:20.783 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:20.785 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
14:00:20.788 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:20.790 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:20.790 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
14:00:20.790 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:20.817 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
14:00:20.818 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	2025-05-27 14:00:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:20.818 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
14:00:20.884 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
14:00:20.884 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
14:00:20.884 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
14:00:20.891 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:20.892 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
14:00:20.892 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:20.893 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:20.893 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
14:00:20.973 INFO  Funcotator - Initializing Funcotator Engine...
14:00:20.973 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:20.973 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:00:20.973 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator18439512961201599583.vcf
14:00:20.975 INFO  ProgressMeter - Starting traversal
14:00:20.975 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:20.985 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
14:00:20.985 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:00:20.985 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:20.987 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2845835264
14:00:20.987 WARN  gatk -   VCF Elapsed Time: 0.997402217s
14:00:20.988 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator18439512961201599583.vcf
14:00:20.989 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
14:00:21.087 INFO  Funcotator - ------------------------------------------------------------
14:00:21.087 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:21.087 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:21.087 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:21.087 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:21.087 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:21 PM GMT
14:00:21.087 INFO  Funcotator - ------------------------------------------------------------
14:00:21.087 INFO  Funcotator - ------------------------------------------------------------
14:00:21.087 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:21.088 INFO  Funcotator - Picard Version: 3.4.0
14:00:21.088 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:21.088 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:21.088 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:21.088 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:21.088 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:21.088 INFO  Funcotator - Deflater: IntelDeflater
14:00:21.088 INFO  Funcotator - Inflater: IntelInflater
14:00:21.088 INFO  Funcotator - GCS max retries/reopens: 20
14:00:21.088 INFO  Funcotator - Requester pays: disabled
14:00:21.088 INFO  Funcotator - Initializing engine
14:00:21.090 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
14:00:21.091 INFO  Funcotator - Done initializing engine
14:00:21.091 INFO  Funcotator - Validating sequence dictionaries...
14:00:21.091 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:21.091 INFO  Funcotator - Initializing data sources...
14:00:21.091 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:21.091 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:21.091 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
14:00:21.092 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
14:00:21.092 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
14:00:21.092 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
14:00:21.092 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
14:00:21.092 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
14:00:21.093 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
14:00:21.093 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
14:00:21.093 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
14:00:21.093 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
14:00:21.093 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
14:00:21.093 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
14:00:21.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:21.094 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
14:00:21.094 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
14:00:21.094 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:21.094 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
14:00:21.094 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
14:00:21.142 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
14:00:21.143 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
14:00:21.189 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
14:00:21.190 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
14:00:21.914 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
14:00:21.914 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:21.915 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:21.917 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
14:00:21.920 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:21.922 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:21.922 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
14:00:21.923 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:21.957 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
14:00:21.958 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	2025-05-27 14:00:21	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:21.958 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
14:00:22.021 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
14:00:22.021 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
14:00:22.021 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
14:00:22.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:22.029 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
14:00:22.029 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:22.030 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:22.030 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
14:00:22.116 INFO  Funcotator - Initializing Funcotator Engine...
14:00:22.116 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:22.116 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.
14:00:22.116 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator49068500200201463.maf
14:00:22.116 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
14:00:22.117 INFO  ProgressMeter - Starting traversal
14:00:22.117 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:22.128 INFO  ProgressMeter -             unmapped              0.0                     1           5454.5
14:00:22.128 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:00:22.128 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:22.128 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:22 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2524971008
14:00:22.128 WARN  gatk -   MAF Elapsed Time: 1.138073535s
14:00:22.231 INFO  Funcotator - ------------------------------------------------------------
14:00:22.231 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:22.231 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:22.231 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:22.231 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:22.231 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:22 PM GMT
14:00:22.231 INFO  Funcotator - ------------------------------------------------------------
14:00:22.231 INFO  Funcotator - ------------------------------------------------------------
14:00:22.231 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:22.231 INFO  Funcotator - Picard Version: 3.4.0
14:00:22.231 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:22.231 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:22.231 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:22.231 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:22.231 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:22.231 INFO  Funcotator - Deflater: IntelDeflater
14:00:22.231 INFO  Funcotator - Inflater: IntelInflater
14:00:22.231 INFO  Funcotator - GCS max retries/reopens: 20
14:00:22.231 INFO  Funcotator - Requester pays: disabled
14:00:22.231 INFO  Funcotator - Initializing engine
14:00:22.261 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
14:00:22.284 INFO  Funcotator - Done initializing engine
14:00:22.284 INFO  Funcotator - Validating sequence dictionaries...
14:00:22.291 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:22.291 INFO  Funcotator - Initializing data sources...
14:00:22.291 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:22.291 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:22.291 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
14:00:22.292 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
14:00:22.292 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
14:00:22.292 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
14:00:22.292 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
14:00:22.292 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
14:00:22.293 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
14:00:22.293 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
14:00:22.293 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
14:00:22.293 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
14:00:22.293 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
14:00:22.294 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
14:00:22.294 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
14:00:22.294 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:22.294 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
14:00:22.294 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
14:00:22.314 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
14:00:22.315 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
14:00:22.361 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
14:00:22.362 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
14:00:22.969 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
14:00:22.969 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:22.970 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:00:22.971 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
14:00:22.973 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:00:22.974 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
14:00:23.038 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
14:00:23.039 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
14:00:23.039 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
14:00:23.046 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
14:00:23.046 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:23.047 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:00:23.047 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
14:00:23.048 INFO  Funcotator - Initializing Funcotator Engine...
14:00:23.052 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:23.052 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator3576774182650026852.vcf
14:00:23.069 INFO  ProgressMeter - Starting traversal
14:00:23.069 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:23.095 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.
14:00:23.096 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:00:23.099 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:23.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:23.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:23.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:23.102 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:23.103 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:23.103 INFO  ProgressMeter -             unmapped              0.0                     5           8823.5
14:00:23.103 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:00:23.103 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:23.115 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:23 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2524971008
14:00:23.115 WARN  gatk -   VCF Elapsed Time: 0.986358598s
14:00:23.116 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator3576774182650026852.vcf
14:00:23.125 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
14:00:23.226 INFO  Funcotator - ------------------------------------------------------------
14:00:23.226 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:23.226 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:23.226 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:23.226 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:23.226 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:23 PM GMT
14:00:23.226 INFO  Funcotator - ------------------------------------------------------------
14:00:23.226 INFO  Funcotator - ------------------------------------------------------------
14:00:23.226 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:23.226 INFO  Funcotator - Picard Version: 3.4.0
14:00:23.226 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:23.226 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:23.226 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:23.226 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:23.226 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:23.226 INFO  Funcotator - Deflater: IntelDeflater
14:00:23.226 INFO  Funcotator - Inflater: IntelInflater
14:00:23.226 INFO  Funcotator - GCS max retries/reopens: 20
14:00:23.226 INFO  Funcotator - Requester pays: disabled
14:00:23.226 INFO  Funcotator - Initializing engine
14:00:23.251 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
14:00:23.285 INFO  Funcotator - Done initializing engine
14:00:23.285 INFO  Funcotator - Validating sequence dictionaries...
14:00:23.297 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:23.297 INFO  Funcotator - Initializing data sources...
14:00:23.297 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:23.297 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:23.298 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
14:00:23.298 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
14:00:23.298 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
14:00:23.298 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
14:00:23.298 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
14:00:23.299 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
14:00:23.299 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
14:00:23.299 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
14:00:23.299 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
14:00:23.299 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
14:00:23.300 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
14:00:23.300 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
14:00:23.300 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
14:00:23.300 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:23.300 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
14:00:23.300 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
14:00:23.328 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
14:00:23.329 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
14:00:23.416 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
14:00:23.417 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
14:00:23.998 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
14:00:23.998 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:23.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:00:24.000 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
14:00:24.002 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:00:24.003 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
14:00:24.069 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
14:00:24.069 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
14:00:24.070 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
14:00:24.078 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
14:00:24.078 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:24.078 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:00:24.079 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
14:00:24.080 INFO  Funcotator - Initializing Funcotator Engine...
14:00:24.083 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:24.083 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator3620405331997072609.maf
14:00:24.085 INFO  ProgressMeter - Starting traversal
14:00:24.085 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:24.107 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.
14:00:24.107 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
14:00:24.109 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:24.112 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:24.112 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
14:00:24.113 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:24.113 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:24.113 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
14:00:24.114 INFO  ProgressMeter -             unmapped              0.0                     5          10344.8
14:00:24.114 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:00:24.114 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:24.114 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:24 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2524971008
14:00:24.114 WARN  gatk -   MAF Elapsed Time: 0.981115246s
14:00:24.209 INFO  Funcotator - ------------------------------------------------------------
14:00:24.209 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:24.209 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:24.209 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:24.209 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:24.209 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:24 PM GMT
14:00:24.209 INFO  Funcotator - ------------------------------------------------------------
14:00:24.209 INFO  Funcotator - ------------------------------------------------------------
14:00:24.209 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:24.209 INFO  Funcotator - Picard Version: 3.4.0
14:00:24.209 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:24.209 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:24.209 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:24.209 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:24.209 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:24.209 INFO  Funcotator - Deflater: IntelDeflater
14:00:24.209 INFO  Funcotator - Inflater: IntelInflater
14:00:24.209 INFO  Funcotator - GCS max retries/reopens: 20
14:00:24.209 INFO  Funcotator - Requester pays: disabled
14:00:24.209 INFO  Funcotator - Initializing engine
14:00:24.211 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
14:00:24.213 INFO  Funcotator - Done initializing engine
14:00:24.213 INFO  Funcotator - Validating sequence dictionaries...
14:00:24.213 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:24.213 INFO  Funcotator - Initializing data sources...
14:00:24.213 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:24.213 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:24.213 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
14:00:24.213 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
14:00:24.214 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
14:00:24.214 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
14:00:24.214 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
14:00:24.214 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
14:00:24.214 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
14:00:24.215 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
14:00:24.215 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
14:00:24.215 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
14:00:24.215 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
14:00:24.215 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
14:00:24.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:24.216 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
14:00:24.216 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
14:00:24.216 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:24.216 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
14:00:24.216 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
14:00:24.237 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
14:00:24.237 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
14:00:24.283 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
14:00:24.284 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
14:00:24.864 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
14:00:24.864 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:24.865 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:24.867 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
14:00:24.869 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:24.871 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:24.872 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
14:00:24.872 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:24.899 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
14:00:24.899 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	2025-05-27 14:00:24	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:24.899 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
14:00:24.938 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
14:00:24.938 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
14:00:24.939 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
14:00:24.947 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:24.947 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
14:00:24.947 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:24.948 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:24.948 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
14:00:25.029 INFO  Funcotator - Initializing Funcotator Engine...
14:00:25.030 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:25.030 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:00:25.030 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator13645794611416500888.vcf
14:00:25.033 INFO  ProgressMeter - Starting traversal
14:00:25.033 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:30.651 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:00:30.652 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:00:30.653 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16089.0
14:00:30.653 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:00:30.653 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:00:30.674 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:30 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=2571108352
14:00:30.674 WARN  gatk -   VCF Elapsed Time: 6.557885103s
14:00:30.675 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator13645794611416500888.vcf
14:00:30.682 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
14:00:30.812 INFO  Funcotator - ------------------------------------------------------------
14:00:30.812 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:30.812 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:30.812 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:30.812 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:30.812 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:30 PM GMT
14:00:30.812 INFO  Funcotator - ------------------------------------------------------------
14:00:30.812 INFO  Funcotator - ------------------------------------------------------------
14:00:30.812 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:30.812 INFO  Funcotator - Picard Version: 3.4.0
14:00:30.812 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:30.812 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:30.812 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:30.812 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:30.812 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:30.812 INFO  Funcotator - Deflater: IntelDeflater
14:00:30.812 INFO  Funcotator - Inflater: IntelInflater
14:00:30.812 INFO  Funcotator - GCS max retries/reopens: 20
14:00:30.812 INFO  Funcotator - Requester pays: disabled
14:00:30.812 INFO  Funcotator - Initializing engine
14:00:30.815 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
14:00:30.816 INFO  Funcotator - Done initializing engine
14:00:30.816 INFO  Funcotator - Validating sequence dictionaries...
14:00:30.816 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:30.816 INFO  Funcotator - Initializing data sources...
14:00:30.816 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:30.816 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:30.817 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
14:00:30.817 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
14:00:30.817 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
14:00:30.817 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
14:00:30.817 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
14:00:30.818 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
14:00:30.818 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
14:00:30.818 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
14:00:30.818 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
14:00:30.818 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
14:00:30.819 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
14:00:30.819 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
14:00:30.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:30.819 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
14:00:30.819 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
14:00:30.819 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:30.819 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
14:00:30.820 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
14:00:30.840 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
14:00:30.841 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
14:00:30.888 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
14:00:30.888 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
14:00:31.492 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
14:00:31.492 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:31.493 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:31.495 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
14:00:31.498 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:31.500 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:31.500 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
14:00:31.501 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:31.528 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
14:00:31.528 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	2025-05-27 14:00:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:31.528 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
14:00:31.567 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
14:00:31.567 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
14:00:31.568 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
14:00:31.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:31.576 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
14:00:31.576 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:31.577 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:31.577 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
14:00:31.658 INFO  Funcotator - Initializing Funcotator Engine...
14:00:31.659 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:31.659 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
14:00:31.659 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator3508375892211837199.maf
14:00:31.659 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
14:00:31.660 INFO  ProgressMeter - Starting traversal
14:00:31.660 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:36.986 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
14:00:36.986 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
14:00:36.987 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16973.9
14:00:36.987 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
14:00:36.987 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
14:00:36.987 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=2571108352
14:00:36.988 WARN  gatk -   MAF Elapsed Time: 6.286907895s
14:00:37.101 INFO  Funcotator - ------------------------------------------------------------
14:00:37.101 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:37.101 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:37.101 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:37.101 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:37.101 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:37 PM GMT
14:00:37.101 INFO  Funcotator - ------------------------------------------------------------
14:00:37.101 INFO  Funcotator - ------------------------------------------------------------
14:00:37.101 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:37.101 INFO  Funcotator - Picard Version: 3.4.0
14:00:37.101 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:37.101 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:37.101 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:37.101 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:37.101 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:37.101 INFO  Funcotator - Deflater: IntelDeflater
14:00:37.101 INFO  Funcotator - Inflater: IntelInflater
14:00:37.101 INFO  Funcotator - GCS max retries/reopens: 20
14:00:37.101 INFO  Funcotator - Requester pays: disabled
14:00:37.102 INFO  Funcotator - Initializing engine
14:00:37.104 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:00:37.105 INFO  Funcotator - Done initializing engine
14:00:37.105 INFO  Funcotator - Validating sequence dictionaries...
14:00:37.105 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:37.105 INFO  Funcotator - Initializing data sources...
14:00:37.105 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:37.105 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:37.106 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
14:00:37.106 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
14:00:37.106 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
14:00:37.106 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
14:00:37.106 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
14:00:37.107 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
14:00:37.107 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
14:00:37.107 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
14:00:37.107 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
14:00:37.107 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
14:00:37.107 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
14:00:37.108 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
14:00:37.108 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:37.108 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
14:00:37.108 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
14:00:37.108 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:37.108 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
14:00:37.108 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
14:00:37.128 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
14:00:37.129 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
14:00:37.211 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
14:00:37.211 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
14:00:37.764 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
14:00:37.764 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:37.765 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:37.767 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
14:00:37.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:37.771 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:37.772 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
14:00:37.772 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:37.799 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
14:00:37.800 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	2025-05-27 14:00:37	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:37.800 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
14:00:37.838 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
14:00:37.839 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
14:00:37.839 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
14:00:37.846 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:37.847 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
14:00:37.847 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:37.848 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:37.848 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
14:00:37.930 INFO  Funcotator - Initializing Funcotator Engine...
14:00:37.930 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:37.930 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.
14:00:37.930 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator5952713515539712572.vcf
14:00:37.932 INFO  ProgressMeter - Starting traversal
14:00:37.932 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:40.003 INFO  ProgressMeter -             unmapped              0.0                   198           5736.4
14:00:40.003 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:00:40.003 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:00:40.011 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:40 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2571108352
14:00:40.118 INFO  Funcotator - ------------------------------------------------------------
14:00:40.118 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:40.118 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:40.118 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:40.118 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:40.118 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:40 PM GMT
14:00:40.118 INFO  Funcotator - ------------------------------------------------------------
14:00:40.118 INFO  Funcotator - ------------------------------------------------------------
14:00:40.118 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:40.119 INFO  Funcotator - Picard Version: 3.4.0
14:00:40.119 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:40.119 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:40.119 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:40.119 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:40.119 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:40.119 INFO  Funcotator - Deflater: IntelDeflater
14:00:40.119 INFO  Funcotator - Inflater: IntelInflater
14:00:40.119 INFO  Funcotator - GCS max retries/reopens: 20
14:00:40.119 INFO  Funcotator - Requester pays: disabled
14:00:40.119 INFO  Funcotator - Initializing engine
14:00:40.121 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:00:40.122 INFO  Funcotator - Done initializing engine
14:00:40.122 INFO  Funcotator - Validating sequence dictionaries...
14:00:40.122 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:40.122 INFO  Funcotator - Initializing data sources...
14:00:40.122 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:40.122 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:40.123 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
14:00:40.123 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
14:00:40.123 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
14:00:40.123 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
14:00:40.123 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
14:00:40.124 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
14:00:40.124 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
14:00:40.124 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
14:00:40.124 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
14:00:40.124 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
14:00:40.124 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
14:00:40.125 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
14:00:40.125 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:40.125 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
14:00:40.125 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
14:00:40.125 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:40.125 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
14:00:40.125 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
14:00:40.146 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
14:00:40.146 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
14:00:40.193 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
14:00:40.193 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
14:00:40.794 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
14:00:40.794 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:40.795 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:40.797 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
14:00:40.800 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:40.802 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:40.802 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
14:00:40.802 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:40.829 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
14:00:40.829 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	2025-05-27 14:00:40	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:40.830 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
14:00:40.869 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
14:00:40.869 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
14:00:40.870 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
14:00:40.877 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:40.877 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
14:00:40.877 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:40.878 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:40.879 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
14:00:40.959 INFO  Funcotator - Initializing Funcotator Engine...
14:00:40.959 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:40.959 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.
14:00:40.959 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator17647336193190595574.maf
14:00:40.960 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
14:00:40.960 INFO  ProgressMeter - Starting traversal
14:00:40.960 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:42.994 INFO  ProgressMeter -             unmapped              0.0                   198           5840.7
14:00:42.994 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:00:42.995 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:00:42.995 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2571108352
14:00:43.093 INFO  Funcotator - ------------------------------------------------------------
14:00:43.093 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:43.093 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:43.093 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:43.093 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:43.093 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:43 PM GMT
14:00:43.093 INFO  Funcotator - ------------------------------------------------------------
14:00:43.093 INFO  Funcotator - ------------------------------------------------------------
14:00:43.093 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:43.093 INFO  Funcotator - Picard Version: 3.4.0
14:00:43.093 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:43.093 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:43.093 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:43.093 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:43.093 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:43.093 INFO  Funcotator - Deflater: IntelDeflater
14:00:43.093 INFO  Funcotator - Inflater: IntelInflater
14:00:43.093 INFO  Funcotator - GCS max retries/reopens: 20
14:00:43.093 INFO  Funcotator - Requester pays: disabled
14:00:43.093 INFO  Funcotator - Initializing engine
14:00:43.095 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
14:00:43.096 INFO  Funcotator - Done initializing engine
14:00:43.096 INFO  Funcotator - Validating sequence dictionaries...
14:00:43.096 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:43.097 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2571108352
14:00:43.195 INFO  Funcotator - ------------------------------------------------------------
14:00:43.195 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:43.195 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:43.195 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:43.195 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:43.195 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:43 PM GMT
14:00:43.195 INFO  Funcotator - ------------------------------------------------------------
14:00:43.195 INFO  Funcotator - ------------------------------------------------------------
14:00:43.195 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:43.195 INFO  Funcotator - Picard Version: 3.4.0
14:00:43.195 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:43.196 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:43.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:43.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:43.196 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:43.196 INFO  Funcotator - Deflater: IntelDeflater
14:00:43.196 INFO  Funcotator - Inflater: IntelInflater
14:00:43.196 INFO  Funcotator - GCS max retries/reopens: 20
14:00:43.196 INFO  Funcotator - Requester pays: disabled
14:00:43.196 INFO  Funcotator - Initializing engine
14:00:43.197 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:00:43.216 INFO  Funcotator - Done initializing engine
14:00:43.216 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:43.216 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:43.216 INFO  Funcotator - Initializing data sources...
14:00:43.216 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:43.216 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:43.216 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
14:00:43.217 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
14:00:43.217 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
14:00:43.217 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:43.217 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
14:00:43.217 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:43.218 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
14:00:43.218 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
14:00:43.219 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
14:00:43.219 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:43.219 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
14:00:43.229 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
14:00:43.238 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
14:00:43.247 INFO  Funcotator - Initializing Funcotator Engine...
14:00:43.254 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:43.254 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11673018317003086214.vcf
14:00:43.266 INFO  ProgressMeter - Starting traversal
14:00:43.267 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:43.298 INFO  ProgressMeter -             unmapped              0.0                   100         193548.4
14:00:43.298 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:00:43.298 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:00:43.304 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2571108352
14:00:43.305 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11673018317003086214.vcf
14:00:43.418 INFO  Funcotator - ------------------------------------------------------------
14:00:43.418 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:43.418 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:43.418 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:43.418 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:43.418 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:43 PM GMT
14:00:43.418 INFO  Funcotator - ------------------------------------------------------------
14:00:43.418 INFO  Funcotator - ------------------------------------------------------------
14:00:43.418 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:43.418 INFO  Funcotator - Picard Version: 3.4.0
14:00:43.418 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:43.418 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:43.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:43.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:43.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:43.418 INFO  Funcotator - Deflater: IntelDeflater
14:00:43.418 INFO  Funcotator - Inflater: IntelInflater
14:00:43.418 INFO  Funcotator - GCS max retries/reopens: 20
14:00:43.418 INFO  Funcotator - Requester pays: disabled
14:00:43.418 INFO  Funcotator - Initializing engine
14:00:43.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:00:43.421 INFO  Funcotator - Done initializing engine
14:00:43.421 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:43.421 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:43.421 INFO  Funcotator - Initializing data sources...
14:00:43.421 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:43.421 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:43.421 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
14:00:43.421 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
14:00:43.421 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
14:00:43.421 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:43.422 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
14:00:43.422 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:43.422 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
14:00:43.422 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
14:00:43.423 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
14:00:43.423 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:43.424 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
14:00:43.424 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
14:00:43.426 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
14:00:43.426 INFO  Funcotator - Initializing Funcotator Engine...
14:00:43.426 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:43.427 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.
14:00:43.427 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3697077783047493274.vcf
14:00:43.430 INFO  ProgressMeter - Starting traversal
14:00:43.430 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:43.445 INFO  ProgressMeter -             unmapped              0.0                    21          84000.0
14:00:43.445 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:00:43.445 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:00:43.448 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2571108352
14:00:43.449 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3697077783047493274.vcf
14:00:43.594 INFO  Funcotator - ------------------------------------------------------------
14:00:43.594 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:43.594 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:43.594 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:43.594 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:43.594 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:43 PM GMT
14:00:43.594 INFO  Funcotator - ------------------------------------------------------------
14:00:43.594 INFO  Funcotator - ------------------------------------------------------------
14:00:43.594 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:43.594 INFO  Funcotator - Picard Version: 3.4.0
14:00:43.594 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:43.594 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:43.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:43.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:43.594 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:43.594 INFO  Funcotator - Deflater: IntelDeflater
14:00:43.594 INFO  Funcotator - Inflater: IntelInflater
14:00:43.594 INFO  Funcotator - GCS max retries/reopens: 20
14:00:43.594 INFO  Funcotator - Requester pays: disabled
14:00:43.594 INFO  Funcotator - Initializing engine
14:00:43.595 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
14:00:43.607 INFO  Funcotator - Done initializing engine
14:00:43.607 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:43.607 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:43.608 INFO  Funcotator - Initializing data sources...
14:00:43.608 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:43.608 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:43.608 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
14:00:43.608 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
14:00:43.608 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
14:00:43.608 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:43.608 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
14:00:43.608 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:43.609 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
14:00:43.609 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
14:00:43.610 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
14:00:43.610 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:43.610 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
14:00:43.618 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
14:00:43.626 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
14:00:43.634 INFO  Funcotator - Initializing Funcotator Engine...
14:00:43.638 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:43.638 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15983666711091147309.vcf
14:00:43.649 INFO  ProgressMeter - Starting traversal
14:00:43.649 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:43.654 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)
14:00:43.654 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)
14:00:43.654 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.654 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:43.654 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:00:43.654 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:00:43.657 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.657 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:43.657 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:00:43.657 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:00:43.657 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)
14:00:43.658 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)
14:00:43.658 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.658 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:43.658 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:00:43.658 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:00:43.659 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)
14:00:43.659 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)
14:00:43.659 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:00:43.659 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:00:43.659 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:00:43.659 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:00:43.660 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.660 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:43.660 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:00:43.661 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:00:43.661 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.661 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:43.662 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:00:43.662 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:00:43.662 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)
14:00:43.663 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)
14:00:43.663 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:00:43.663 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:43.663 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:00:43.663 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:00:43.663 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)
14:00:43.664 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)
14:00:43.664 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.664 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:43.664 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:00:43.664 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:00:43.665 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:00:43.665 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:43.665 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:00:43.665 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:00:43.666 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)
14:00:43.666 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)
14:00:43.666 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:43.666 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:43.666 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:00:43.666 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:00:43.667 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
14:00:43.667 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:00:43.667 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:43.672 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2571108352
14:00:43.673 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15983666711091147309.vcf
14:00:43.776 INFO  Funcotator - ------------------------------------------------------------
14:00:43.776 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:43.776 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:43.776 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:43.776 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:43.776 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:43 PM GMT
14:00:43.776 INFO  Funcotator - ------------------------------------------------------------
14:00:43.776 INFO  Funcotator - ------------------------------------------------------------
14:00:43.776 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:43.776 INFO  Funcotator - Picard Version: 3.4.0
14:00:43.776 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:43.776 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:43.776 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:43.776 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:43.776 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:43.776 INFO  Funcotator - Deflater: IntelDeflater
14:00:43.776 INFO  Funcotator - Inflater: IntelInflater
14:00:43.776 INFO  Funcotator - GCS max retries/reopens: 20
14:00:43.776 INFO  Funcotator - Requester pays: disabled
14:00:43.776 INFO  Funcotator - Initializing engine
14:00:43.779 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
14:00:43.781 INFO  Funcotator - Done initializing engine
14:00:43.781 INFO  Funcotator - Validating sequence dictionaries...
14:00:43.781 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:43.781 INFO  Funcotator - Initializing data sources...
14:00:43.781 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:43.781 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:43.782 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
14:00:43.782 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
14:00:43.782 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
14:00:43.782 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
14:00:43.783 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
14:00:43.783 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
14:00:43.783 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
14:00:43.783 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
14:00:43.783 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
14:00:43.784 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
14:00:43.784 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
14:00:43.784 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
14:00:43.784 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:43.784 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
14:00:43.784 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
14:00:43.784 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:43.785 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
14:00:43.785 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
14:00:43.809 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
14:00:43.810 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
14:00:43.856 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
14:00:43.857 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
14:00:44.473 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
14:00:44.473 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:44.475 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:44.476 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
14:00:44.479 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:44.481 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:44.481 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
14:00:44.482 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:44.509 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
14:00:44.509 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	2025-05-27 14:00:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:44.510 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
14:00:44.547 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
14:00:44.548 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
14:00:44.548 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
14:00:44.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:44.556 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
14:00:44.556 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:44.556 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:44.557 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
14:00:44.640 INFO  Funcotator - Initializing Funcotator Engine...
14:00:44.640 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:44.640 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.
14:00:44.641 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator12135062324112640238.vcf
14:00:44.644 INFO  ProgressMeter - Starting traversal
14:00:44.644 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:44.694 INFO  ProgressMeter -             unmapped              0.0                     1           1200.0
14:00:44.694 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:00:44.694 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:44.695 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2571108352
14:00:44.695 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator12135062324112640238.vcf
14:00:44.793 INFO  Funcotator - ------------------------------------------------------------
14:00:44.793 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:44.793 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:44.793 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:44.793 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:44.793 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:44 PM GMT
14:00:44.793 INFO  Funcotator - ------------------------------------------------------------
14:00:44.793 INFO  Funcotator - ------------------------------------------------------------
14:00:44.793 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:44.793 INFO  Funcotator - Picard Version: 3.4.0
14:00:44.793 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:44.793 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:44.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:44.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:44.793 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:44.793 INFO  Funcotator - Deflater: IntelDeflater
14:00:44.793 INFO  Funcotator - Inflater: IntelInflater
14:00:44.793 INFO  Funcotator - GCS max retries/reopens: 20
14:00:44.793 INFO  Funcotator - Requester pays: disabled
14:00:44.793 INFO  Funcotator - Initializing engine
14:00:44.795 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
14:00:44.796 INFO  Funcotator - Done initializing engine
14:00:44.797 INFO  Funcotator - Validating sequence dictionaries...
14:00:44.797 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:44.797 INFO  Funcotator - Initializing data sources...
14:00:44.797 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:44.797 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:44.797 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
14:00:44.797 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
14:00:44.797 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
14:00:44.797 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
14:00:44.798 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
14:00:44.798 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
14:00:44.798 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
14:00:44.798 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
14:00:44.798 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
14:00:44.798 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
14:00:44.799 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
14:00:44.799 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
14:00:44.799 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:44.799 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
14:00:44.799 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
14:00:44.799 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:44.799 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
14:00:44.800 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
14:00:44.820 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
14:00:44.821 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
14:00:44.867 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
14:00:44.868 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
14:00:45.560 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
14:00:45.560 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:45.561 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:45.563 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
14:00:45.566 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:45.568 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:45.568 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
14:00:45.569 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:45.596 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
14:00:45.596 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	2025-05-27 14:00:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:45.596 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
14:00:45.634 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
14:00:45.634 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
14:00:45.635 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
14:00:45.642 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:45.642 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
14:00:45.642 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:45.643 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:45.644 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
14:00:45.723 INFO  Funcotator - Initializing Funcotator Engine...
14:00:45.724 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:45.724 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.
14:00:45.724 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator5182315844025602609.vcf
14:00:45.727 INFO  ProgressMeter - Starting traversal
14:00:45.727 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:45.734 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
14:00:45.773 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.773 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.773 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.774 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.774 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.774 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.774 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
14:00:45.777 INFO  ProgressMeter -             unmapped              0.0                     2           2400.0
14:00:45.777 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:00:45.777 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:45.778 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2571108352
14:00:45.778 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator5182315844025602609.vcf
14:00:45.924 INFO  Funcotator - ------------------------------------------------------------
14:00:45.924 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:45.924 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:45.924 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:45.924 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:45.924 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:45 PM GMT
14:00:45.924 INFO  Funcotator - ------------------------------------------------------------
14:00:45.924 INFO  Funcotator - ------------------------------------------------------------
14:00:45.924 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:45.924 INFO  Funcotator - Picard Version: 3.4.0
14:00:45.924 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:45.924 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:45.924 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:45.924 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:45.924 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:45.924 INFO  Funcotator - Deflater: IntelDeflater
14:00:45.924 INFO  Funcotator - Inflater: IntelInflater
14:00:45.924 INFO  Funcotator - GCS max retries/reopens: 20
14:00:45.924 INFO  Funcotator - Requester pays: disabled
14:00:45.924 INFO  Funcotator - Initializing engine
14:00:45.926 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
14:00:45.927 INFO  Funcotator - Done initializing engine
14:00:45.927 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:45.927 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:45.927 INFO  Funcotator - Initializing data sources...
14:00:45.927 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:45.927 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:45.928 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
14:00:45.928 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
14:00:45.928 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
14:00:45.928 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
14:00:45.929 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
14:00:45.929 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
14:00:45.929 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
14:00:45.929 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
14:00:45.929 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
14:00:45.929 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
14:00:45.930 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
14:00:45.930 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
14:00:45.930 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:45.930 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
14:00:45.930 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
14:00:45.930 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:45.931 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
14:00:45.931 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
14:00:45.951 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
14:00:45.951 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
14:00:45.997 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
14:00:45.997 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
14:00:46.669 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
14:00:46.669 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:46.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:46.672 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
14:00:46.675 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:46.677 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:46.677 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
14:00:46.677 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:46.705 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
14:00:46.705 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	2025-05-27 14:00:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:46.705 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
14:00:46.743 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
14:00:46.744 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
14:00:46.744 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
14:00:46.751 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:46.751 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
14:00:46.751 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:46.752 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:46.753 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
14:00:46.868 INFO  Funcotator - Initializing Funcotator Engine...
14:00:46.868 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:46.868 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.
14:00:46.868 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
14:00:46.868 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
14:00:46.869 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
14:00:46.869 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out8091604243803644031.vcf
14:00:46.872 INFO  ProgressMeter - Starting traversal
14:00:46.872 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:46.907 INFO  ProgressMeter -             unmapped              0.0                     1           1714.3
14:00:46.907 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:00:46.907 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:46.907 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2734686208
14:00:46.908 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out8091604243803644031.vcf
14:00:46.909 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_expected_out.vcf
[May 27, 2025 at 2:00:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2734686208
[May 27, 2025 at 2:00:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2734686208
14:00:47.278 INFO  Funcotator - ------------------------------------------------------------
14:00:47.278 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:47.278 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:47.278 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:47.278 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:47.278 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:47 PM GMT
14:00:47.278 INFO  Funcotator - ------------------------------------------------------------
14:00:47.278 INFO  Funcotator - ------------------------------------------------------------
14:00:47.278 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:47.278 INFO  Funcotator - Picard Version: 3.4.0
14:00:47.278 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:47.278 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:47.278 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:47.278 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:47.278 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:47.278 INFO  Funcotator - Deflater: IntelDeflater
14:00:47.278 INFO  Funcotator - Inflater: IntelInflater
14:00:47.278 INFO  Funcotator - GCS max retries/reopens: 20
14:00:47.278 INFO  Funcotator - Requester pays: disabled
14:00:47.278 INFO  Funcotator - Initializing engine
14:00:47.279 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:00:47.295 INFO  Funcotator - Done initializing engine
14:00:47.296 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:47.296 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:47.296 INFO  Funcotator - Initializing data sources...
14:00:47.296 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:47.296 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:47.296 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
14:00:47.296 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
14:00:47.296 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
14:00:47.296 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:47.296 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
14:00:47.296 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:47.297 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
14:00:47.297 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
14:00:47.298 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
14:00:47.298 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:47.298 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
14:00:47.306 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
14:00:47.315 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
14:00:47.323 INFO  Funcotator - Initializing Funcotator Engine...
14:00:47.330 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:47.330 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out49443095765277597.vcf
14:00:47.342 INFO  ProgressMeter - Starting traversal
14:00:47.342 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:47.366 INFO  ProgressMeter -             unmapped              0.0                   100         250000.0
14:00:47.367 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:00:47.367 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:00:47.372 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2734686208
14:00:47.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out49443095765277597.vcf
14:00:47.489 INFO  Funcotator - ------------------------------------------------------------
14:00:47.489 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:47.489 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:47.489 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:47.489 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:47.489 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:47 PM GMT
14:00:47.489 INFO  Funcotator - ------------------------------------------------------------
14:00:47.489 INFO  Funcotator - ------------------------------------------------------------
14:00:47.489 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:47.489 INFO  Funcotator - Picard Version: 3.4.0
14:00:47.489 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:47.489 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:47.489 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:47.489 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:47.489 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:47.489 INFO  Funcotator - Deflater: IntelDeflater
14:00:47.489 INFO  Funcotator - Inflater: IntelInflater
14:00:47.489 INFO  Funcotator - GCS max retries/reopens: 20
14:00:47.489 INFO  Funcotator - Requester pays: disabled
14:00:47.489 INFO  Funcotator - Initializing engine
14:00:47.491 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
14:00:47.492 INFO  Funcotator - Done initializing engine
14:00:47.492 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:47.492 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:47.492 INFO  Funcotator - Initializing data sources...
14:00:47.492 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/
14:00:47.492 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:47.492 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
14:00:47.493 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
14:00:47.493 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
14:00:47.493 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:47.493 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
14:00:47.493 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:00:47.493 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
14:00:47.495 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
14:00:47.498 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
14:00:47.500 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
14:00:47.500 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:47.501 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
14:00:47.502 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
14:00:47.502 INFO  Funcotator - Initializing Funcotator Engine...
14:00:47.502 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:47.502 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.
14:00:47.502 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:47.502 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing12246226160185586488.vcf
14:00:47.505 INFO  ProgressMeter - Starting traversal
14:00:47.505 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:47.527 INFO  ProgressMeter -             unmapped              0.0                     1           2727.3
14:00:47.527 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:00:47.527 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
14:00:47.530 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2734686208
14:00:47.530 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing12246226160185586488.vcf
14:00:47.624 INFO  Funcotator - ------------------------------------------------------------
14:00:47.624 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:47.624 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:47.624 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:47.624 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:47.624 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:47 PM GMT
14:00:47.624 INFO  Funcotator - ------------------------------------------------------------
14:00:47.624 INFO  Funcotator - ------------------------------------------------------------
14:00:47.625 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:47.625 INFO  Funcotator - Picard Version: 3.4.0
14:00:47.625 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:47.625 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:47.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:47.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:47.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:47.625 INFO  Funcotator - Deflater: IntelDeflater
14:00:47.625 INFO  Funcotator - Inflater: IntelInflater
14:00:47.625 INFO  Funcotator - GCS max retries/reopens: 20
14:00:47.625 INFO  Funcotator - Requester pays: disabled
14:00:47.625 INFO  Funcotator - Initializing engine
14:00:47.626 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:47.626 INFO  Funcotator - Done initializing engine
14:00:47.626 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:47.626 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:47.626 INFO  Funcotator - Initializing data sources...
14:00:47.626 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:47.626 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:47.627 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
14:00:47.627 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
14:00:47.627 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/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
14:00:47.627 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
14:00:47.627 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
14:00:47.627 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
14:00:47.628 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
14:00:47.628 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
14:00:47.628 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
14:00:47.628 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
14:00:47.628 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
14:00:47.629 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
14:00:47.629 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:47.629 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
14:00:47.629 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
14:00:47.629 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:47.629 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
14:00:47.629 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
14:00:47.649 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
14:00:47.650 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
14:00:47.712 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
14:00:47.712 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
14:00:48.366 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
14:00:48.366 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:48.368 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:48.370 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
14:00:48.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:48.375 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:48.375 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
14:00:48.376 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:48.403 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
14:00:48.403 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	2025-05-27 14:00:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:48.403 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
14:00:48.470 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
14:00:48.471 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
14:00:48.471 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
14:00:48.478 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:48.479 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
14:00:48.479 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:48.479 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:48.480 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
14:00:48.560 INFO  Funcotator - Initializing Funcotator Engine...
14:00:48.560 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
14:00:48.560 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:48.560 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:48.560 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:48.560 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:48.561 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:48.561 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:48.561 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3421965417234519875.vcf
14:00:48.561 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
14:00:48.562 INFO  ProgressMeter - Starting traversal
14:00:48.562 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:48.583 INFO  ProgressMeter -             unmapped              0.0                     3           8571.4
14:00:48.583 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:48.584 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:48.586 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:48 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2854223872
14:00:48.679 INFO  Funcotator - ------------------------------------------------------------
14:00:48.679 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:48.680 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:48.680 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:48.680 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:48.680 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:48 PM GMT
14:00:48.680 INFO  Funcotator - ------------------------------------------------------------
14:00:48.680 INFO  Funcotator - ------------------------------------------------------------
14:00:48.680 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:48.680 INFO  Funcotator - Picard Version: 3.4.0
14:00:48.680 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:48.680 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:48.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:48.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:48.680 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:48.680 INFO  Funcotator - Deflater: IntelDeflater
14:00:48.680 INFO  Funcotator - Inflater: IntelInflater
14:00:48.680 INFO  Funcotator - GCS max retries/reopens: 20
14:00:48.680 INFO  Funcotator - Requester pays: disabled
14:00:48.680 INFO  Funcotator - Initializing engine
14:00:48.681 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:48.681 INFO  Funcotator - Done initializing engine
14:00:48.681 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:48.681 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:48.681 INFO  Funcotator - Initializing data sources...
14:00:48.681 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:48.681 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:48.682 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
14:00:48.682 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
14:00:48.682 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
14:00:48.682 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
14:00:48.682 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
14:00:48.682 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
14:00:48.683 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
14:00:48.683 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
14:00:48.683 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
14:00:48.683 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
14:00:48.683 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
14:00:48.684 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
14:00:48.684 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:48.684 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
14:00:48.684 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
14:00:48.684 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:48.684 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
14:00:48.684 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
14:00:48.738 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
14:00:48.739 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
14:00:48.784 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
14:00:48.785 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
14:00:49.518 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
14:00:49.518 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:49.520 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:49.523 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
14:00:49.526 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:49.528 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:49.528 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
14:00:49.528 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:49.555 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
14:00:49.556 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	2025-05-27 14:00:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:49.556 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
14:00:49.594 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
14:00:49.594 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
14:00:49.594 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
14:00:49.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:49.602 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
14:00:49.602 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:49.603 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:49.603 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
14:00:49.686 INFO  Funcotator - Initializing Funcotator Engine...
14:00:49.686 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:49.686 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:49.686 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16993979427524024275.vcf
14:00:49.687 INFO  ProgressMeter - Starting traversal
14:00:49.687 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:49.795 INFO  ProgressMeter -             unmapped              0.0                     4           2222.2
14:00:49.795 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:49.796 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:49.796 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:49 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2348810240
14:00:49.891 INFO  Funcotator - ------------------------------------------------------------
14:00:49.891 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:49.891 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:49.891 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:49.891 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:49.891 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:49 PM GMT
14:00:49.891 INFO  Funcotator - ------------------------------------------------------------
14:00:49.891 INFO  Funcotator - ------------------------------------------------------------
14:00:49.891 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:49.891 INFO  Funcotator - Picard Version: 3.4.0
14:00:49.891 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:49.891 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:49.891 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:49.891 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:49.891 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:49.891 INFO  Funcotator - Deflater: IntelDeflater
14:00:49.891 INFO  Funcotator - Inflater: IntelInflater
14:00:49.891 INFO  Funcotator - GCS max retries/reopens: 20
14:00:49.891 INFO  Funcotator - Requester pays: disabled
14:00:49.891 INFO  Funcotator - Initializing engine
14:00:49.892 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:49.893 INFO  Funcotator - Done initializing engine
14:00:49.893 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:49.893 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:49.893 INFO  Funcotator - Initializing data sources...
14:00:49.893 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:49.893 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:49.893 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
14:00:49.893 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
14:00:49.893 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
14:00:49.894 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
14:00:49.894 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
14:00:49.894 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
14:00:49.894 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
14:00:49.894 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
14:00:49.894 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
14:00:49.895 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
14:00:49.895 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
14:00:49.895 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
14:00:49.895 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:49.895 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
14:00:49.895 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
14:00:49.895 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:49.895 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
14:00:49.896 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
14:00:49.915 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
14:00:49.916 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
14:00:49.962 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
14:00:49.963 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
14:00:50.639 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
14:00:50.639 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:50.640 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:50.642 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
14:00:50.645 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:50.647 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:50.647 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
14:00:50.648 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:50.675 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
14:00:50.675 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	2025-05-27 14:00:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:50.675 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
14:00:50.714 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
14:00:50.714 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
14:00:50.715 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
14:00:50.722 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:50.723 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
14:00:50.723 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:50.724 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:50.724 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
14:00:50.811 INFO  Funcotator - Initializing Funcotator Engine...
14:00:50.812 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
14:00:50.812 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:50.812 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:50.812 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:50.812 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:50.813 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:50.813 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:50.813 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18109355209939295295.vcf
14:00:50.813 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
14:00:50.814 INFO  ProgressMeter - Starting traversal
14:00:50.814 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:50.836 INFO  ProgressMeter -             unmapped              0.0                     3           8181.8
14:00:50.836 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:50.836 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:50.838 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2348810240
14:00:50.937 INFO  Funcotator - ------------------------------------------------------------
14:00:50.937 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:50.937 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:50.937 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:50.937 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:50.937 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:50 PM GMT
14:00:50.937 INFO  Funcotator - ------------------------------------------------------------
14:00:50.937 INFO  Funcotator - ------------------------------------------------------------
14:00:50.938 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:50.938 INFO  Funcotator - Picard Version: 3.4.0
14:00:50.938 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:50.938 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:50.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:50.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:50.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:50.938 INFO  Funcotator - Deflater: IntelDeflater
14:00:50.938 INFO  Funcotator - Inflater: IntelInflater
14:00:50.938 INFO  Funcotator - GCS max retries/reopens: 20
14:00:50.938 INFO  Funcotator - Requester pays: disabled
14:00:50.938 INFO  Funcotator - Initializing engine
14:00:50.938 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:50.939 INFO  Funcotator - Done initializing engine
14:00:50.939 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:50.939 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:50.939 INFO  Funcotator - Initializing data sources...
14:00:50.939 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:50.939 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:50.939 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
14:00:50.940 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
14:00:50.940 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
14:00:50.940 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
14:00:50.940 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
14:00:50.940 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
14:00:50.940 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
14:00:50.941 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
14:00:50.941 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
14:00:50.941 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
14:00:50.941 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
14:00:50.941 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
14:00:50.941 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:50.942 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
14:00:50.942 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
14:00:50.942 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:50.942 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
14:00:50.942 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
14:00:50.962 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
14:00:50.962 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
14:00:51.010 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
14:00:51.010 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
14:00:51.685 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
14:00:51.685 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:51.686 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:51.688 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
14:00:51.691 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:51.693 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:51.693 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
14:00:51.693 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:51.721 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
14:00:51.721 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	2025-05-27 14:00:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:51.721 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
14:00:51.762 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
14:00:51.762 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
14:00:51.762 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
14:00:51.770 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:51.770 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
14:00:51.771 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:51.771 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:51.772 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
14:00:51.857 INFO  Funcotator - Initializing Funcotator Engine...
14:00:51.857 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:51.857 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:51.857 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5974137426254978436.vcf
14:00:51.858 INFO  ProgressMeter - Starting traversal
14:00:51.858 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:51.966 INFO  ProgressMeter -             unmapped              0.0                     4           2222.2
14:00:51.966 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:51.966 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:51.966 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2489319424
14:00:52.063 INFO  Funcotator - ------------------------------------------------------------
14:00:52.063 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:52.063 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:52.063 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:52.063 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:52.063 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:52 PM GMT
14:00:52.063 INFO  Funcotator - ------------------------------------------------------------
14:00:52.063 INFO  Funcotator - ------------------------------------------------------------
14:00:52.064 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:52.064 INFO  Funcotator - Picard Version: 3.4.0
14:00:52.064 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:52.064 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:52.064 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:52.064 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:52.064 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:52.064 INFO  Funcotator - Deflater: IntelDeflater
14:00:52.064 INFO  Funcotator - Inflater: IntelInflater
14:00:52.064 INFO  Funcotator - GCS max retries/reopens: 20
14:00:52.064 INFO  Funcotator - Requester pays: disabled
14:00:52.064 INFO  Funcotator - Initializing engine
14:00:52.065 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:52.065 INFO  Funcotator - Done initializing engine
14:00:52.065 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:52.065 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:52.065 INFO  Funcotator - Initializing data sources...
14:00:52.065 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:52.065 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:52.066 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
14:00:52.066 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
14:00:52.066 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
14:00:52.066 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
14:00:52.066 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
14:00:52.067 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
14:00:52.067 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
14:00:52.067 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
14:00:52.067 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
14:00:52.067 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
14:00:52.067 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
14:00:52.068 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
14:00:52.068 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:52.068 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
14:00:52.068 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
14:00:52.068 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:52.068 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
14:00:52.068 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
14:00:52.089 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
14:00:52.090 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
14:00:52.136 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
14:00:52.137 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
14:00:52.798 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
14:00:52.798 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:52.799 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:52.801 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
14:00:52.804 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:52.806 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:52.806 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
14:00:52.806 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:52.834 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
14:00:52.834 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	2025-05-27 14:00:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:52.834 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
14:00:52.872 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
14:00:52.872 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
14:00:52.873 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
14:00:52.880 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:52.880 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
14:00:52.880 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:52.881 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:52.882 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
14:00:52.962 INFO  Funcotator - Initializing Funcotator Engine...
14:00:52.962 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
14:00:52.962 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:52.962 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:52.962 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:52.962 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:52.962 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:52.962 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:52.962 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:52.962 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:52.963 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:52.963 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:52.963 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17070892394710963478.maf
14:00:52.963 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
14:00:52.964 INFO  ProgressMeter - Starting traversal
14:00:52.964 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:52.983 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
14:00:52.983 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:52.983 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:52.983 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:52 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2489319424
14:00:53.121 INFO  Funcotator - ------------------------------------------------------------
14:00:53.121 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:53.121 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:53.121 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:53.121 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:53.121 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:53 PM GMT
14:00:53.121 INFO  Funcotator - ------------------------------------------------------------
14:00:53.121 INFO  Funcotator - ------------------------------------------------------------
14:00:53.121 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:53.121 INFO  Funcotator - Picard Version: 3.4.0
14:00:53.121 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:53.121 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:53.121 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:53.121 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:53.121 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:53.121 INFO  Funcotator - Deflater: IntelDeflater
14:00:53.121 INFO  Funcotator - Inflater: IntelInflater
14:00:53.121 INFO  Funcotator - GCS max retries/reopens: 20
14:00:53.121 INFO  Funcotator - Requester pays: disabled
14:00:53.121 INFO  Funcotator - Initializing engine
14:00:53.122 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:53.123 INFO  Funcotator - Done initializing engine
14:00:53.123 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:53.123 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:53.123 INFO  Funcotator - Initializing data sources...
14:00:53.123 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:53.123 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:53.123 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
14:00:53.123 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
14:00:53.124 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
14:00:53.124 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
14:00:53.124 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
14:00:53.124 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
14:00:53.124 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
14:00:53.124 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
14:00:53.125 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
14:00:53.125 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
14:00:53.125 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
14:00:53.125 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
14:00:53.125 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:53.125 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
14:00:53.125 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
14:00:53.125 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:53.126 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
14:00:53.126 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
14:00:53.150 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
14:00:53.150 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
14:00:53.200 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
14:00:53.201 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
14:00:53.831 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
14:00:53.831 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:53.832 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:53.834 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
14:00:53.836 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:53.838 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:53.839 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
14:00:53.839 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:53.866 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
14:00:53.866 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	2025-05-27 14:00:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:53.867 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
14:00:53.905 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
14:00:53.905 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
14:00:53.906 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
14:00:53.913 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:53.913 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
14:00:53.913 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:53.914 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:53.914 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
14:00:53.995 INFO  Funcotator - Initializing Funcotator Engine...
14:00:53.995 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:53.995 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:53.995 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10451694892576561940.maf
14:00:53.995 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:00:53.996 INFO  ProgressMeter - Starting traversal
14:00:53.996 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:54.102 INFO  ProgressMeter -             unmapped              0.0                     4           2264.2
14:00:54.102 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:54.102 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:54.102 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2596274176
14:00:54.243 INFO  Funcotator - ------------------------------------------------------------
14:00:54.243 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:54.243 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:54.243 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:54.243 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:54.243 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:54 PM GMT
14:00:54.243 INFO  Funcotator - ------------------------------------------------------------
14:00:54.243 INFO  Funcotator - ------------------------------------------------------------
14:00:54.243 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:54.243 INFO  Funcotator - Picard Version: 3.4.0
14:00:54.243 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:54.243 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:54.243 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:54.243 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:54.243 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:54.243 INFO  Funcotator - Deflater: IntelDeflater
14:00:54.243 INFO  Funcotator - Inflater: IntelInflater
14:00:54.243 INFO  Funcotator - GCS max retries/reopens: 20
14:00:54.243 INFO  Funcotator - Requester pays: disabled
14:00:54.243 INFO  Funcotator - Initializing engine
14:00:54.244 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
14:00:54.245 INFO  Funcotator - Done initializing engine
14:00:54.245 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:54.245 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:54.245 INFO  Funcotator - Initializing data sources...
14:00:54.245 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:54.245 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:54.245 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
14:00:54.245 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
14:00:54.245 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
14:00:54.246 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
14:00:54.246 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
14:00:54.246 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
14:00:54.246 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
14:00:54.246 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
14:00:54.246 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
14:00:54.246 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
14:00:54.247 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
14:00:54.247 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
14:00:54.247 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:54.247 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
14:00:54.247 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
14:00:54.247 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:54.247 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
14:00:54.247 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
14:00:54.267 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
14:00:54.268 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
14:00:54.314 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
14:00:54.315 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
14:00:54.944 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
14:00:54.944 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:54.945 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:54.947 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
14:00:54.949 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:54.951 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:54.952 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
14:00:54.952 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:54.979 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
14:00:54.979 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
WARNING	2025-05-27 14:00:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:54.980 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
14:00:55.043 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
14:00:55.043 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
14:00:55.044 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
14:00:55.051 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:55.051 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
14:00:55.051 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:55.052 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:55.053 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
14:00:55.132 INFO  Funcotator - Initializing Funcotator Engine...
14:00:55.132 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
14:00:55.132 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
14:00:55.132 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:00:55.132 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
14:00:55.132 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
14:00:55.133 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
14:00:55.133 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:55.133 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6640825829339219659.maf
14:00:55.133 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
14:00:55.134 INFO  ProgressMeter - Starting traversal
14:00:55.134 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:55.153 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
14:00:55.153 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
14:00:55.153 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:00:55.153 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:55 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2675965952
14:00:55.245 INFO  Funcotator - ------------------------------------------------------------
14:00:55.245 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:55.245 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:55.245 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:55.245 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:55.245 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:55 PM GMT
14:00:55.245 INFO  Funcotator - ------------------------------------------------------------
14:00:55.245 INFO  Funcotator - ------------------------------------------------------------
14:00:55.245 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:55.245 INFO  Funcotator - Picard Version: 3.4.0
14:00:55.245 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:55.245 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:55.245 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:55.245 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:55.245 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:55.245 INFO  Funcotator - Deflater: IntelDeflater
14:00:55.245 INFO  Funcotator - Inflater: IntelInflater
14:00:55.245 INFO  Funcotator - GCS max retries/reopens: 20
14:00:55.245 INFO  Funcotator - Requester pays: disabled
14:00:55.245 INFO  Funcotator - Initializing engine
14:00:55.246 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
14:00:55.246 INFO  Funcotator - Done initializing engine
14:00:55.246 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:55.246 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:55.246 INFO  Funcotator - Initializing data sources...
14:00:55.247 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:55.247 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:55.247 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
14:00:55.247 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
14:00:55.247 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
14:00:55.247 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
14:00:55.247 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
14:00:55.248 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
14:00:55.248 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
14:00:55.248 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
14:00:55.248 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
14:00:55.248 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
14:00:55.248 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
14:00:55.248 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
14:00:55.249 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:55.249 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
14:00:55.249 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
14:00:55.249 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:55.249 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
14:00:55.249 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
14:00:55.305 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
14:00:55.306 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
14:00:55.352 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
14:00:55.353 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
14:00:56.059 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
14:00:56.059 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:56.060 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:56.062 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
14:00:56.065 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:56.067 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:56.067 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
14:00:56.068 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:56.096 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
14:00:56.096 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	2025-05-27 14:00:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:56.096 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
14:00:56.134 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
14:00:56.134 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
14:00:56.134 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
14:00:56.141 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:56.142 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
14:00:56.142 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:56.142 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:56.143 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
14:00:56.223 INFO  Funcotator - Initializing Funcotator Engine...
14:00:56.223 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:00:56.223 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:56.223 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16506763106333620007.maf
14:00:56.223 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
14:00:56.224 INFO  ProgressMeter - Starting traversal
14:00:56.224 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:56.328 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
14:00:56.328 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:00:56.328 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
14:00:56.329 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2866806784
14:00:56.422 INFO  Funcotator - ------------------------------------------------------------
14:00:56.422 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:56.422 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:56.422 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:56.422 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:56.422 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:56 PM GMT
14:00:56.422 INFO  Funcotator - ------------------------------------------------------------
14:00:56.422 INFO  Funcotator - ------------------------------------------------------------
14:00:56.422 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:56.422 INFO  Funcotator - Picard Version: 3.4.0
14:00:56.422 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:56.422 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:56.422 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:56.422 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:56.422 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:56.422 INFO  Funcotator - Deflater: IntelDeflater
14:00:56.422 INFO  Funcotator - Inflater: IntelInflater
14:00:56.422 INFO  Funcotator - GCS max retries/reopens: 20
14:00:56.422 INFO  Funcotator - Requester pays: disabled
14:00:56.422 INFO  Funcotator - Initializing engine
14:00:56.423 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:00:56.447 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:00:56.447 INFO  Funcotator - Done initializing engine
14:00:56.447 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:56.447 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:56.447 INFO  Funcotator - Initializing data sources...
14:00:56.447 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
14:00:56.447 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:56.447 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
14:00:56.448 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
14:00:56.448 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
14:00:56.448 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:56.448 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
14:00:56.448 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:56.449 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
14:00:56.457 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
14:00:56.465 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
14:00:56.473 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
14:00:56.473 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:56.474 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
14:00:56.475 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
14:00:56.475 INFO  Funcotator - Initializing Funcotator Engine...
14:00:56.480 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:56.480 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1765768464186187141.vcf
14:00:56.492 INFO  ProgressMeter - Starting traversal
14:00:56.492 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:56.504 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
14:00:56.504 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:00:56.504 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:00:56.509 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:56.601 INFO  Funcotator - ------------------------------------------------------------
14:00:56.601 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:56.601 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:56.601 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:56.601 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:56.601 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:56 PM GMT
14:00:56.601 INFO  Funcotator - ------------------------------------------------------------
14:00:56.601 INFO  Funcotator - ------------------------------------------------------------
14:00:56.601 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:56.601 INFO  Funcotator - Picard Version: 3.4.0
14:00:56.601 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:56.601 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:56.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:56.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:56.601 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:56.601 INFO  Funcotator - Deflater: IntelDeflater
14:00:56.601 INFO  Funcotator - Inflater: IntelInflater
14:00:56.601 INFO  Funcotator - GCS max retries/reopens: 20
14:00:56.601 INFO  Funcotator - Requester pays: disabled
14:00:56.601 INFO  Funcotator - Initializing engine
14:00:56.602 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:00:56.623 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
14:00:56.623 INFO  Funcotator - Done initializing engine
14:00:56.623 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:56.623 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:56.623 INFO  Funcotator - Initializing data sources...
14:00:56.623 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
14:00:56.623 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:56.624 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
14:00:56.624 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
14:00:56.624 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
14:00:56.624 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:56.624 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
14:00:56.624 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:56.625 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
14:00:56.633 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
14:00:56.688 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
14:00:56.735 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
14:00:56.735 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:56.736 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
14:00:56.736 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
14:00:56.737 INFO  Funcotator - Initializing Funcotator Engine...
14:00:56.743 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:56.743 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2882524310143834173.vcf
14:00:56.755 INFO  ProgressMeter - Starting traversal
14:00:56.755 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:56.766 INFO  ProgressMeter -             unmapped              0.0                    32         174545.5
14:00:56.766 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
14:00:56.766 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:00:56.771 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:56.771 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1765768464186187141.vcf
14:00:56.781 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2882524310143834173.vcf
14:00:56.887 INFO  Funcotator - ------------------------------------------------------------
14:00:56.887 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:56.887 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:56.887 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:56.887 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:56.887 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:56 PM GMT
14:00:56.887 INFO  Funcotator - ------------------------------------------------------------
14:00:56.887 INFO  Funcotator - ------------------------------------------------------------
14:00:56.887 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:56.887 INFO  Funcotator - Picard Version: 3.4.0
14:00:56.887 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:56.887 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:56.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:56.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:56.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:56.887 INFO  Funcotator - Deflater: IntelDeflater
14:00:56.887 INFO  Funcotator - Inflater: IntelInflater
14:00:56.887 INFO  Funcotator - GCS max retries/reopens: 20
14:00:56.887 INFO  Funcotator - Requester pays: disabled
14:00:56.887 INFO  Funcotator - Initializing engine
14:00:56.888 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
14:00:56.890 INFO  Funcotator - Done initializing engine
14:00:56.890 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:56.890 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:56.890 INFO  Funcotator - Initializing data sources...
14:00:56.890 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:56.890 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:56.890 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
14:00:56.890 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
14:00:56.890 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
14:00:56.890 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:56.890 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
14:00:56.890 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:56.891 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
14:00:56.891 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
14:00:56.891 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
14:00:56.891 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:56.892 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
14:00:56.893 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
14:00:56.894 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
14:00:56.895 INFO  Funcotator - Initializing Funcotator Engine...
14:00:56.895 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:56.895 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.
14:00:56.895 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out883556293916071478.maf
14:00:56.895 INFO  ProgressMeter - Starting traversal
14:00:56.895 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:56.897 WARN  MafOutputRenderer - 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
14:00:56.898 WARN  MafOutputRenderer - 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
14:00:56.898 WARN  MafOutputRenderer - 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
14:00:56.899 WARN  MafOutputRenderer - 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=
14:00:56.899 WARN  MafOutputRenderer - 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=
14:00:56.901 WARN  MafOutputRenderer - 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=
14:00:56.901 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
14:00:56.901 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:00:56.901 WARN  Funcotator - ================================================================================
14:00:56.901 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:00:56.901 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:00:56.901 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:00:56.901 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:00:56.901 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:00:56.901 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:00:56.901 WARN  Funcotator - --------------------------------------------------------------------------------
14:00:56.901 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:00:56.901 WARN  Funcotator -  run was misconfigured.     
14:00:56.901 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:00:56.901 WARN  Funcotator - ================================================================================
14:00:56.901 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:56.901 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:56.997 INFO  Funcotator - ------------------------------------------------------------
14:00:56.997 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:56.997 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:56.997 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:56.997 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:56.997 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:56 PM GMT
14:00:56.997 INFO  Funcotator - ------------------------------------------------------------
14:00:56.997 INFO  Funcotator - ------------------------------------------------------------
14:00:56.997 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:56.997 INFO  Funcotator - Picard Version: 3.4.0
14:00:56.997 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:56.997 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:56.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:56.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:56.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:56.997 INFO  Funcotator - Deflater: IntelDeflater
14:00:56.997 INFO  Funcotator - Inflater: IntelInflater
14:00:56.997 INFO  Funcotator - GCS max retries/reopens: 20
14:00:56.997 INFO  Funcotator - Requester pays: disabled
14:00:56.997 INFO  Funcotator - Initializing engine
14:00:56.998 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
14:00:56.999 INFO  Funcotator - Done initializing engine
14:00:56.999 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:56.999 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:56.999 INFO  Funcotator - Initializing data sources...
14:00:56.999 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:56.999 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:56.999 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
14:00:56.999 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
14:00:56.999 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
14:00:57.000 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.000 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
14:00:57.000 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.000 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
14:00:57.000 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
14:00:57.001 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
14:00:57.001 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.001 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
14:00:57.002 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
14:00:57.004 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
14:00:57.004 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.005 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:57.005 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.
14:00:57.005 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13392924599414346430.maf
14:00:57.005 INFO  ProgressMeter - Starting traversal
14:00:57.005 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:57.007 WARN  MafOutputRenderer - 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
14:00:57.007 WARN  MafOutputRenderer - 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
14:00:57.008 WARN  MafOutputRenderer - 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
14:00:57.009 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:00:57.009 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:00:57.010 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:00:57.011 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
14:00:57.011 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:00:57.011 WARN  Funcotator - ================================================================================
14:00:57.011 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:00:57.011 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:00:57.011 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:00:57.011 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:00:57.011 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:00:57.011 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:00:57.011 WARN  Funcotator - --------------------------------------------------------------------------------
14:00:57.011 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:00:57.011 WARN  Funcotator -  run was misconfigured.     
14:00:57.011 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:00:57.011 WARN  Funcotator - ================================================================================
14:00:57.011 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:57.011 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.115 INFO  Funcotator - ------------------------------------------------------------
14:00:57.115 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.115 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.115 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.115 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.115 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.115 INFO  Funcotator - ------------------------------------------------------------
14:00:57.115 INFO  Funcotator - ------------------------------------------------------------
14:00:57.115 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.115 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.115 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.115 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.115 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.115 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.115 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.115 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.115 INFO  Funcotator - Inflater: IntelInflater
14:00:57.115 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.115 INFO  Funcotator - Requester pays: disabled
14:00:57.115 INFO  Funcotator - Initializing engine
14:00:57.116 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
14:00:57.117 INFO  Funcotator - Done initializing engine
14:00:57.117 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:57.117 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.117 INFO  Funcotator - Initializing data sources...
14:00:57.117 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:57.117 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.117 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
14:00:57.117 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
14:00:57.118 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
14:00:57.118 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.118 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
14:00:57.118 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.118 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
14:00:57.118 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
14:00:57.119 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
14:00:57.119 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.119 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
14:00:57.120 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
14:00:57.121 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
14:00:57.122 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.122 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:57.122 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.
14:00:57.122 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5651450103163412850.maf
14:00:57.123 INFO  ProgressMeter - Starting traversal
14:00:57.123 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:57.124 WARN  MafOutputRenderer - 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
14:00:57.125 WARN  MafOutputRenderer - 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
14:00:57.125 WARN  MafOutputRenderer - 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
14:00:57.127 WARN  MafOutputRenderer - 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=
14:00:57.127 WARN  MafOutputRenderer - 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=
14:00:57.128 WARN  MafOutputRenderer - 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=
14:00:57.128 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
14:00:57.128 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:00:57.128 WARN  Funcotator - ================================================================================
14:00:57.128 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:00:57.128 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:00:57.128 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:00:57.128 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:00:57.128 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:00:57.128 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:00:57.128 WARN  Funcotator - --------------------------------------------------------------------------------
14:00:57.128 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:00:57.128 WARN  Funcotator -  run was misconfigured.     
14:00:57.128 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:00:57.128 WARN  Funcotator - ================================================================================
14:00:57.128 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:57.128 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.229 INFO  Funcotator - ------------------------------------------------------------
14:00:57.229 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.229 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.229 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.229 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.229 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.229 INFO  Funcotator - ------------------------------------------------------------
14:00:57.229 INFO  Funcotator - ------------------------------------------------------------
14:00:57.229 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.229 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.229 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.229 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.229 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.229 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.229 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.229 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.229 INFO  Funcotator - Inflater: IntelInflater
14:00:57.229 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.229 INFO  Funcotator - Requester pays: disabled
14:00:57.229 INFO  Funcotator - Initializing engine
14:00:57.230 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
14:00:57.231 INFO  Funcotator - Done initializing engine
14:00:57.231 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:57.231 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.231 INFO  Funcotator - Initializing data sources...
14:00:57.231 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:57.231 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.231 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
14:00:57.231 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
14:00:57.232 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
14:00:57.232 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.232 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
14:00:57.232 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.232 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
14:00:57.232 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
14:00:57.233 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
14:00:57.233 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.233 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
14:00:57.234 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
14:00:57.235 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
14:00:57.236 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.236 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:57.236 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.
14:00:57.236 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13462515862810775497.maf
14:00:57.237 INFO  ProgressMeter - Starting traversal
14:00:57.237 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:57.238 WARN  MafOutputRenderer - 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
14:00:57.238 WARN  MafOutputRenderer - 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
14:00:57.239 WARN  MafOutputRenderer - 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
14:00:57.240 WARN  MafOutputRenderer - 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=
14:00:57.240 WARN  MafOutputRenderer - 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=
14:00:57.241 WARN  MafOutputRenderer - 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=
14:00:57.241 INFO  ProgressMeter -             unmapped              0.0                     6          90000.0
14:00:57.241 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
14:00:57.241 WARN  Funcotator - ================================================================================
14:00:57.241 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:00:57.241 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:00:57.241 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:00:57.241 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:00:57.241 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:00:57.241 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:00:57.241 WARN  Funcotator - --------------------------------------------------------------------------------
14:00:57.241 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:00:57.241 WARN  Funcotator -  run was misconfigured.     
14:00:57.241 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:00:57.241 WARN  Funcotator - ================================================================================
14:00:57.241 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:57.242 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.339 INFO  Funcotator - ------------------------------------------------------------
14:00:57.339 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.339 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.339 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.339 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.339 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.339 INFO  Funcotator - ------------------------------------------------------------
14:00:57.339 INFO  Funcotator - ------------------------------------------------------------
14:00:57.339 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.339 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.339 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.339 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.339 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.339 INFO  Funcotator - Inflater: IntelInflater
14:00:57.339 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.339 INFO  Funcotator - Requester pays: disabled
14:00:57.339 INFO  Funcotator - Initializing engine
14:00:57.340 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:00:57.342 INFO  Funcotator - Done initializing engine
14:00:57.342 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:57.342 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.342 INFO  Funcotator - Initializing data sources...
14:00:57.342 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:57.342 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.342 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
14:00:57.342 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
14:00:57.342 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
14:00:57.342 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.342 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
14:00:57.342 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.343 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
14:00:57.343 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
14:00:57.344 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
14:00:57.344 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.344 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
14:00:57.345 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
14:00:57.346 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
14:00:57.347 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.347 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:57.347 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.
14:00:57.347 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9046667514758074845.vcf
14:00:57.351 INFO  ProgressMeter - Starting traversal
14:00:57.351 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:57.361 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:00:57.361 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:00:57.361 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:00:57.363 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.364 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9046667514758074845.vcf
14:00:57.465 INFO  Funcotator - ------------------------------------------------------------
14:00:57.465 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.465 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.465 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.465 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.465 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.465 INFO  Funcotator - ------------------------------------------------------------
14:00:57.465 INFO  Funcotator - ------------------------------------------------------------
14:00:57.465 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.465 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.465 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.465 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.465 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.465 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.465 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.465 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.465 INFO  Funcotator - Inflater: IntelInflater
14:00:57.465 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.465 INFO  Funcotator - Requester pays: disabled
14:00:57.465 INFO  Funcotator - Initializing engine
14:00:57.466 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
14:00:57.467 INFO  Funcotator - Done initializing engine
14:00:57.467 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:57.467 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.467 INFO  Funcotator - Initializing data sources...
14:00:57.467 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:57.467 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.467 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
14:00:57.467 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
14:00:57.467 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
14:00:57.467 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.467 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
14:00:57.467 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.468 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
14:00:57.468 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
14:00:57.468 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
14:00:57.468 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.469 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
14:00:57.470 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
14:00:57.471 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
14:00:57.472 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.472 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:00:57.472 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.
14:00:57.472 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12714560093007606242.maf
14:00:57.472 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:57.472 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.565 INFO  Funcotator - ------------------------------------------------------------
14:00:57.565 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.565 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.565 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.565 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.565 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.565 INFO  Funcotator - ------------------------------------------------------------
14:00:57.565 INFO  Funcotator - ------------------------------------------------------------
14:00:57.566 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.566 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.566 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.566 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.566 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.566 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.566 INFO  Funcotator - Inflater: IntelInflater
14:00:57.566 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.566 INFO  Funcotator - Requester pays: disabled
14:00:57.566 INFO  Funcotator - Initializing engine
14:00:57.566 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
14:00:57.579 INFO  Funcotator - Done initializing engine
14:00:57.579 INFO  Funcotator - Skipping sequence dictionary validation.
14:00:57.579 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.579 INFO  Funcotator - Initializing data sources...
14:00:57.579 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:00:57.579 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.579 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
14:00:57.579 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
14:00:57.579 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
14:00:57.579 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.579 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
14:00:57.579 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:57.580 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
14:00:57.580 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
14:00:57.581 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
14:00:57.581 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:00:57.581 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
14:00:57.589 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
14:00:57.597 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
14:00:57.605 INFO  Funcotator - Initializing Funcotator Engine...
14:00:57.609 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:00:57.609 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7785032739219766068.maf
14:00:57.610 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
14:00:57.610 INFO  ProgressMeter - Starting traversal
14:00:57.610 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:00:57.613 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)
14:00:57.614 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)
14:00:57.614 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.614 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:57.614 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:00:57.614 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
14:00:57.616 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:00:57.619 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.619 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:57.619 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:00:57.619 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
14:00:57.619 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:00:57.620 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)
14:00:57.620 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)
14:00:57.620 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.620 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:57.620 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:00:57.620 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
14:00:57.620 WARN  MafOutputRenderer - 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+
14:00:57.621 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)
14:00:57.621 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)
14:00:57.621 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
14:00:57.621 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
14:00:57.621 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:00:57.621 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
14:00:57.621 WARN  MafOutputRenderer - 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+
14:00:57.622 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.622 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:57.622 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:00:57.622 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
14:00:57.622 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:00:57.623 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.623 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:57.623 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:00:57.623 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
14:00:57.623 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:00:57.624 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)
14:00:57.624 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)
14:00:57.624 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:00:57.624 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:57.624 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:00:57.624 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
14:00:57.624 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:00:57.625 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)
14:00:57.625 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)
14:00:57.625 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.625 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:57.625 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:00:57.625 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
14:00:57.625 WARN  MafOutputRenderer - 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+
14:00:57.626 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
14:00:57.626 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
14:00:57.626 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:00:57.626 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
14:00:57.626 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:00:57.627 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)
14:00:57.627 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)
14:00:57.627 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
14:00:57.627 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
14:00:57.627 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:00:57.627 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
14:00:57.627 WARN  MafOutputRenderer - 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=
14:00:57.628 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
14:00:57.628 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:00:57.628 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
14:00:57.628 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.823 INFO  Funcotator - ------------------------------------------------------------
14:00:57.823 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.823 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.823 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.823 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.823 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.823 INFO  Funcotator - ------------------------------------------------------------
14:00:57.823 INFO  Funcotator - ------------------------------------------------------------
14:00:57.823 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.823 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.823 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.823 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.823 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.823 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.823 INFO  Funcotator - Inflater: IntelInflater
14:00:57.823 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.823 INFO  Funcotator - Requester pays: disabled
14:00:57.823 INFO  Funcotator - Initializing engine
14:00:57.824 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
14:00:57.825 INFO  Funcotator - Done initializing engine
14:00:57.825 INFO  Funcotator - Validating sequence dictionaries...
14:00:57.825 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:00:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:00:57.915 INFO  Funcotator - ------------------------------------------------------------
14:00:57.915 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:00:57.915 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:00:57.915 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:00:57.915 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:00:57.915 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:00:57 PM GMT
14:00:57.915 INFO  Funcotator - ------------------------------------------------------------
14:00:57.915 INFO  Funcotator - ------------------------------------------------------------
14:00:57.915 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:00:57.915 INFO  Funcotator - Picard Version: 3.4.0
14:00:57.915 INFO  Funcotator - Built for Spark Version: 3.5.0
14:00:57.915 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:00:57.915 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:00:57.915 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:00:57.915 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:00:57.915 INFO  Funcotator - Deflater: IntelDeflater
14:00:57.915 INFO  Funcotator - Inflater: IntelInflater
14:00:57.915 INFO  Funcotator - GCS max retries/reopens: 20
14:00:57.915 INFO  Funcotator - Requester pays: disabled
14:00:57.915 INFO  Funcotator - Initializing engine
14:00:57.917 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:00:57.918 INFO  Funcotator - Done initializing engine
14:00:57.918 INFO  Funcotator - Validating sequence dictionaries...
14:00:57.918 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:00:57.918 INFO  Funcotator - Initializing data sources...
14:00:57.918 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:00:57.918 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:00:57.919 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
14:00:57.919 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
14:00:57.919 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
14:00:57.919 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
14:00:57.919 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
14:00:57.919 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
14:00:57.920 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
14:00:57.920 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
14:00:57.920 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
14:00:57.920 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
14:00:57.920 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
14:00:57.920 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
14:00:57.921 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:57.921 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
14:00:57.921 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
14:00:57.921 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:00:57.921 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
14:00:57.921 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
14:00:57.941 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
14:00:57.942 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
14:00:58.003 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
14:00:58.003 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
14:00:58.550 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
14:00:58.550 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:00:58.551 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:58.553 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
14:00:58.556 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:00:58.558 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:00:58.558 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
14:00:58.558 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:00:58.630 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
14:00:58.630 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	2025-05-27 14:00:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:00:58.631 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
14:00:58.670 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
14:00:58.670 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
14:00:58.670 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
14:00:58.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:00:58.678 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
14:00:58.678 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:00:58.679 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:00:58.679 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
14:00:58.759 INFO  Funcotator - Initializing Funcotator Engine...
14:00:58.759 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:00:58.759 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.
14:00:58.759 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator17143834461766096364.vcf
14:00:58.761 INFO  ProgressMeter - Starting traversal
14:00:58.761 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:00.790 INFO  ProgressMeter -             unmapped              0.0                   198           5855.1
14:01:00.790 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:01:00.790 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:01:00.798 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2866806784
14:01:00.890 INFO  Funcotator - ------------------------------------------------------------
14:01:00.890 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:00.890 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:00.890 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:00.890 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:00.890 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:00 PM GMT
14:01:00.890 INFO  Funcotator - ------------------------------------------------------------
14:01:00.890 INFO  Funcotator - ------------------------------------------------------------
14:01:00.890 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:00.890 INFO  Funcotator - Picard Version: 3.4.0
14:01:00.890 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:00.890 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:00.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:00.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:00.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:00.891 INFO  Funcotator - Deflater: IntelDeflater
14:01:00.891 INFO  Funcotator - Inflater: IntelInflater
14:01:00.891 INFO  Funcotator - GCS max retries/reopens: 20
14:01:00.891 INFO  Funcotator - Requester pays: disabled
14:01:00.891 INFO  Funcotator - Initializing engine
14:01:00.893 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
14:01:00.893 INFO  Funcotator - Done initializing engine
14:01:00.893 INFO  Funcotator - Validating sequence dictionaries...
14:01:00.894 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:00.894 INFO  Funcotator - Initializing data sources...
14:01:00.894 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:01:00.894 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:00.894 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
14:01:00.894 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
14:01:00.894 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
14:01:00.894 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
14:01:00.895 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
14:01:00.895 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
14:01:00.895 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
14:01:00.895 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
14:01:00.895 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
14:01:00.895 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
14:01:00.895 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
14:01:00.896 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
14:01:00.896 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:00.896 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
14:01:00.896 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
14:01:00.896 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:00.896 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
14:01:00.896 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
14:01:00.917 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
14:01:00.917 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
14:01:00.964 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
14:01:00.965 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
14:01:01.543 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
14:01:01.544 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:01:01.545 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:01.547 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
14:01:01.549 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:01.551 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:01:01.552 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
14:01:01.552 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:01:01.579 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
14:01:01.580 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	2025-05-27 14:01:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:01:01.580 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
14:01:01.618 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
14:01:01.618 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
14:01:01.618 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
14:01:01.626 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:01.626 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
14:01:01.626 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:01.627 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:01:01.627 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
14:01:01.772 INFO  Funcotator - Initializing Funcotator Engine...
14:01:01.772 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
14:01:01.772 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.
14:01:01.772 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator16551524471013856171.maf
14:01:01.773 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
14:01:01.773 INFO  ProgressMeter - Starting traversal
14:01:01.773 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:03.752 INFO  ProgressMeter -             unmapped              0.0                   198           6003.0
14:01:03.752 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
14:01:03.752 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
14:01:03.753 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:03 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2866806784
14:01:03.846 INFO  Funcotator - ------------------------------------------------------------
14:01:03.846 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:03.846 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:03.846 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:03.846 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:03.846 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:03 PM GMT
14:01:03.846 INFO  Funcotator - ------------------------------------------------------------
14:01:03.846 INFO  Funcotator - ------------------------------------------------------------
14:01:03.847 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:03.847 INFO  Funcotator - Picard Version: 3.4.0
14:01:03.847 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:03.847 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:03.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:03.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:03.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:03.847 INFO  Funcotator - Deflater: IntelDeflater
14:01:03.847 INFO  Funcotator - Inflater: IntelInflater
14:01:03.847 INFO  Funcotator - GCS max retries/reopens: 20
14:01:03.847 INFO  Funcotator - Requester pays: disabled
14:01:03.847 INFO  Funcotator - Initializing engine
14:01:03.872 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
14:01:03.893 INFO  Funcotator - Done initializing engine
14:01:03.893 INFO  Funcotator - Validating sequence dictionaries...
14:01:03.899 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:03.899 INFO  Funcotator - Initializing data sources...
14:01:03.899 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:01:03.899 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:03.900 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
14:01:03.900 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
14:01:03.900 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
14:01:03.900 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
14:01:03.900 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
14:01:03.901 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
14:01:03.901 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
14:01:03.901 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
14:01:03.901 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
14:01:03.901 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
14:01:03.901 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
14:01:03.901 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
14:01:03.902 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
14:01:03.902 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:03.902 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
14:01:03.902 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
14:01:03.922 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
14:01:03.922 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
14:01:03.990 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
14:01:03.991 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
14:01:04.564 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
14:01:04.564 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:01:04.565 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:01:04.566 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
14:01:04.568 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
14:01:04.569 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
14:01:04.633 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
14:01:04.633 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
14:01:04.634 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
14:01:04.641 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
14:01:04.641 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:04.641 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
14:01:04.642 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
14:01:04.643 INFO  Funcotator - Initializing Funcotator Engine...
14:01:04.646 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:01:04.646 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator6792224969776095857.vcf
14:01:04.647 INFO  ProgressMeter - Starting traversal
14:01:04.647 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:04.652 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
14:01:04.655 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2866806784
14:01:04.749 INFO  Funcotator - ------------------------------------------------------------
14:01:04.749 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:04.749 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:04.749 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:04.749 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:04.749 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:04 PM GMT
14:01:04.749 INFO  Funcotator - ------------------------------------------------------------
14:01:04.749 INFO  Funcotator - ------------------------------------------------------------
14:01:04.749 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:04.749 INFO  Funcotator - Picard Version: 3.4.0
14:01:04.749 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:04.749 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:04.749 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:04.749 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:04.749 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:04.749 INFO  Funcotator - Deflater: IntelDeflater
14:01:04.749 INFO  Funcotator - Inflater: IntelInflater
14:01:04.749 INFO  Funcotator - GCS max retries/reopens: 20
14:01:04.749 INFO  Funcotator - Requester pays: disabled
14:01:04.749 INFO  Funcotator - Initializing engine
14:01:04.751 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
14:01:04.752 INFO  Funcotator - Done initializing engine
14:01:04.752 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:04.752 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:04.752 INFO  Funcotator - Initializing data sources...
14:01:04.752 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
14:01:04.752 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:04.752 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
14:01:04.752 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
14:01:04.752 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
14:01:04.752 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:04.752 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
14:01:04.752 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
14:01:04.753 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:01:04.753 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
14:01:04.754 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
14:01:04.754 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
14:01:04.754 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:04.755 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
14:01:04.755 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
14:01:04.756 INFO  Funcotator - Initializing Funcotator Engine...
14:01:04.756 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:04.756 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.
14:01:04.756 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:04.756 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing4911435262703240518.vcf
14:01:04.756 INFO  ProgressMeter - Starting traversal
14:01:04.756 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:04.761 INFO  ProgressMeter -             unmapped              0.0                     1          12000.0
14:01:04.761 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:01:04.761 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
14:01:04.763 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:04.764 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing4911435262703240518.vcf
14:01:04.858 INFO  Funcotator - ------------------------------------------------------------
14:01:04.858 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:04.858 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:04.858 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:04.858 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:04.858 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:04 PM GMT
14:01:04.858 INFO  Funcotator - ------------------------------------------------------------
14:01:04.858 INFO  Funcotator - ------------------------------------------------------------
14:01:04.858 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:04.858 INFO  Funcotator - Picard Version: 3.4.0
14:01:04.858 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:04.858 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:04.858 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:04.858 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:04.858 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:04.858 INFO  Funcotator - Deflater: IntelDeflater
14:01:04.858 INFO  Funcotator - Inflater: IntelInflater
14:01:04.858 INFO  Funcotator - GCS max retries/reopens: 20
14:01:04.858 INFO  Funcotator - Requester pays: disabled
14:01:04.858 INFO  Funcotator - Initializing engine
14:01:04.859 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:01:04.860 INFO  Funcotator - Done initializing engine
14:01:04.860 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:04.860 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:04.860 INFO  Funcotator - Initializing data sources...
14:01:04.860 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:04.860 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:04.861 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
14:01:04.861 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
14:01:04.861 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
14:01:04.861 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:04.861 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
14:01:04.861 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:04.862 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
14:01:04.862 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
14:01:04.862 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
14:01:04.862 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:04.863 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
14:01:04.863 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
14:01:04.864 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
14:01:04.865 INFO  Funcotator - Initializing Funcotator Engine...
14:01:04.865 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:04.865 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.
14:01:04.865 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11603013208364213375.maf
14:01:04.866 INFO  ProgressMeter - Starting traversal
14:01:04.866 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:04.868 WARN  MafOutputRenderer - 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=
14:01:04.869 WARN  MafOutputRenderer - 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=
14:01:04.869 WARN  MafOutputRenderer - 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=
14:01:04.870 WARN  MafOutputRenderer - 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=
14:01:04.871 WARN  MafOutputRenderer - 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=
14:01:04.871 WARN  MafOutputRenderer - 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=
14:01:04.871 WARN  MafOutputRenderer - 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=
14:01:04.872 WARN  MafOutputRenderer - 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=
14:01:04.872 WARN  MafOutputRenderer - 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=
14:01:04.873 WARN  MafOutputRenderer - 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=
14:01:04.873 WARN  MafOutputRenderer - 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=
14:01:04.874 WARN  MafOutputRenderer - 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=
14:01:04.874 WARN  MafOutputRenderer - 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=
14:01:04.874 WARN  MafOutputRenderer - 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=
14:01:04.875 WARN  MafOutputRenderer - 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=
14:01:04.875 WARN  MafOutputRenderer - 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=
14:01:04.875 WARN  MafOutputRenderer - 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=
14:01:04.876 WARN  MafOutputRenderer - 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=
14:01:04.876 WARN  MafOutputRenderer - 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=
14:01:04.876 WARN  MafOutputRenderer - 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=
14:01:04.876 WARN  MafOutputRenderer - 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=
14:01:04.876 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:01:04.876 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:01:04.877 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:01:04.877 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:04.879 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:01:04.881 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:01:04.980 INFO  Funcotator - ------------------------------------------------------------
14:01:04.980 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:04.980 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:04.980 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:04.980 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:04.980 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:04 PM GMT
14:01:04.980 INFO  Funcotator - ------------------------------------------------------------
14:01:04.980 INFO  Funcotator - ------------------------------------------------------------
14:01:04.980 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:04.980 INFO  Funcotator - Picard Version: 3.4.0
14:01:04.980 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:04.980 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:04.980 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:04.980 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:04.980 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:04.980 INFO  Funcotator - Deflater: IntelDeflater
14:01:04.980 INFO  Funcotator - Inflater: IntelInflater
14:01:04.980 INFO  Funcotator - GCS max retries/reopens: 20
14:01:04.980 INFO  Funcotator - Requester pays: disabled
14:01:04.980 INFO  Funcotator - Initializing engine
14:01:04.981 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:01:04.982 INFO  Funcotator - Done initializing engine
14:01:04.982 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:04.982 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:04.982 INFO  Funcotator - Initializing data sources...
14:01:04.982 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:04.982 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:04.982 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
14:01:04.982 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
14:01:04.983 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
14:01:04.983 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:04.983 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
14:01:04.983 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:04.983 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
14:01:04.984 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
14:01:04.984 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
14:01:04.984 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:04.984 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
14:01:04.985 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
14:01:04.986 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
14:01:04.987 INFO  Funcotator - Initializing Funcotator Engine...
14:01:04.987 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:04.987 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.
14:01:04.987 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9259584557147697993.vcf
14:01:04.991 INFO  ProgressMeter - Starting traversal
14:01:04.991 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:04.999 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
14:01:04.999 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:01:04.999 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:01:05.001 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.002 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9259584557147697993.vcf
14:01:05.139 INFO  Funcotator - ------------------------------------------------------------
14:01:05.139 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.139 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.139 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.139 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.139 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.139 INFO  Funcotator - ------------------------------------------------------------
14:01:05.139 INFO  Funcotator - ------------------------------------------------------------
14:01:05.139 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.139 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.139 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.139 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.139 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.139 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.139 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.139 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.139 INFO  Funcotator - Inflater: IntelInflater
14:01:05.139 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.139 INFO  Funcotator - Requester pays: disabled
14:01:05.139 INFO  Funcotator - Initializing engine
14:01:05.140 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
14:01:05.140 INFO  Funcotator - Done initializing engine
14:01:05.140 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.140 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.140 INFO  Funcotator - Initializing data sources...
14:01:05.141 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:05.141 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.141 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
14:01:05.141 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
14:01:05.141 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
14:01:05.141 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.141 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
14:01:05.141 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:05.142 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
14:01:05.142 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
14:01:05.142 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
14:01:05.142 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:05.143 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
14:01:05.143 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
14:01:05.145 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
14:01:05.145 INFO  Funcotator - Initializing Funcotator Engine...
14:01:05.145 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:05.145 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.
14:01:05.145 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:05.145 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3070529980811132553.vcf
14:01:05.146 INFO  ProgressMeter - Starting traversal
14:01:05.146 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:05.150 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
14:01:05.150 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
14:01:05.150 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:01:05.153 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.153 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3070529980811132553.vcf
14:01:05.254 INFO  Funcotator - ------------------------------------------------------------
14:01:05.254 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.254 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.254 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.254 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.254 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.254 INFO  Funcotator - ------------------------------------------------------------
14:01:05.254 INFO  Funcotator - ------------------------------------------------------------
14:01:05.254 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.254 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.254 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.254 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.254 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.254 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.254 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.254 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.254 INFO  Funcotator - Inflater: IntelInflater
14:01:05.254 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.254 INFO  Funcotator - Requester pays: disabled
14:01:05.254 INFO  Funcotator - Initializing engine
14:01:05.255 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
14:01:05.256 INFO  Funcotator - Done initializing engine
14:01:05.256 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.256 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.256 INFO  Funcotator - Initializing data sources...
14:01:05.256 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:05.256 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.256 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
14:01:05.256 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
14:01:05.256 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
14:01:05.256 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.256 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
14:01:05.256 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:05.257 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
14:01:05.257 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
14:01:05.258 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
14:01:05.258 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:05.258 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
14:01:05.259 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
14:01:05.260 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
14:01:05.261 INFO  Funcotator - Initializing Funcotator Engine...
14:01:05.261 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:05.261 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.
14:01:05.261 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:05.261 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4968185607104093922.vcf
14:01:05.262 INFO  ProgressMeter - Starting traversal
14:01:05.262 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:05.269 INFO  ProgressMeter -             unmapped              0.0                    15         128571.4
14:01:05.269 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:01:05.269 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:01:05.271 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.365 INFO  Funcotator - ------------------------------------------------------------
14:01:05.365 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.365 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.365 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.365 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.366 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.366 INFO  Funcotator - ------------------------------------------------------------
14:01:05.366 INFO  Funcotator - ------------------------------------------------------------
14:01:05.366 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.366 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.366 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.366 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.366 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.366 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.366 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.366 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.366 INFO  Funcotator - Inflater: IntelInflater
14:01:05.366 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.366 INFO  Funcotator - Requester pays: disabled
14:01:05.366 INFO  Funcotator - Initializing engine
14:01:05.367 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
14:01:05.367 INFO  Funcotator - Done initializing engine
14:01:05.367 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.367 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.367 INFO  Funcotator - Initializing data sources...
14:01:05.367 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:05.368 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.368 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
14:01:05.368 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
14:01:05.368 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
14:01:05.368 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.368 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
14:01:05.368 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:05.369 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
14:01:05.369 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
14:01:05.370 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
14:01:05.370 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:05.370 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
14:01:05.371 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
14:01:05.373 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
14:01:05.374 INFO  Funcotator - Initializing Funcotator Engine...
14:01:05.374 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:05.374 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.
14:01:05.374 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:05.374 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12793056965423776109.maf
14:01:05.374 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
14:01:05.374 INFO  ProgressMeter - Starting traversal
14:01:05.374 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:05.377 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
14:01:05.377 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:01:05.378 WARN  MafOutputRenderer - 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=
14:01:05.379 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
14:01:05.379 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
14:01:05.379 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
14:01:05.380 WARN  MafOutputRenderer - 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=
14:01:05.380 WARN  MafOutputRenderer - 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=
14:01:05.380 WARN  MafOutputRenderer - 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=
14:01:05.381 WARN  MafOutputRenderer - 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=
14:01:05.381 WARN  MafOutputRenderer - 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=
14:01:05.381 WARN  MafOutputRenderer - 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=
14:01:05.382 WARN  MafOutputRenderer - 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=
14:01:05.382 WARN  MafOutputRenderer - 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=
14:01:05.382 WARN  MafOutputRenderer - 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=
14:01:05.383 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
14:01:05.383 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
14:01:05.383 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
14:01:05.383 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.384 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4968185607104093922.vcf
14:01:05.495 INFO  Funcotator - ------------------------------------------------------------
14:01:05.495 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.495 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.495 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.495 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.495 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.495 INFO  Funcotator - ------------------------------------------------------------
14:01:05.495 INFO  Funcotator - ------------------------------------------------------------
14:01:05.495 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.495 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.495 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.495 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.495 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.495 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.495 INFO  Funcotator - Inflater: IntelInflater
14:01:05.495 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.495 INFO  Funcotator - Requester pays: disabled
14:01:05.495 INFO  Funcotator - Initializing engine
14:01:05.496 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:01:05.497 INFO  Funcotator - Done initializing engine
14:01:05.497 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.497 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.497 INFO  Funcotator - Initializing data sources...
14:01:05.497 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:05.497 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.497 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
14:01:05.497 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
14:01:05.497 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
14:01:05.497 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.497 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
14:01:05.498 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:05.498 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
14:01:05.498 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
14:01:05.499 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
14:01:05.499 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:05.499 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
14:01:05.500 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
14:01:05.501 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
14:01:05.502 INFO  Funcotator - Initializing Funcotator Engine...
14:01:05.502 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:05.502 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.
14:01:05.502 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:05.502 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12491879616010561344.vcf
14:01:05.503 INFO  ProgressMeter - Starting traversal
14:01:05.503 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:05.532 INFO  ProgressMeter -             unmapped              0.0                    57         117931.0
14:01:05.532 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:01:05.533 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:05.535 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.657 INFO  Funcotator - ------------------------------------------------------------
14:01:05.657 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.657 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.657 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.657 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.657 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.657 INFO  Funcotator - ------------------------------------------------------------
14:01:05.657 INFO  Funcotator - ------------------------------------------------------------
14:01:05.657 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.657 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.657 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.657 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.657 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.657 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.657 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.657 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.657 INFO  Funcotator - Inflater: IntelInflater
14:01:05.657 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.657 INFO  Funcotator - Requester pays: disabled
14:01:05.657 INFO  Funcotator - Initializing engine
14:01:05.658 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:01:05.659 INFO  Funcotator - Done initializing engine
14:01:05.659 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.659 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.659 INFO  Funcotator - Initializing data sources...
14:01:05.659 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:05.659 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.659 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
14:01:05.659 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
14:01:05.659 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
14:01:05.659 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.659 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
14:01:05.659 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:05.660 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
14:01:05.660 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
14:01:05.660 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
14:01:05.660 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:05.661 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
14:01:05.662 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
14:01:05.663 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
14:01:05.663 INFO  Funcotator - Initializing Funcotator Engine...
14:01:05.664 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:05.664 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.
14:01:05.664 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:05.664 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10934939614721350474.maf
14:01:05.664 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
14:01:05.664 INFO  ProgressMeter - Starting traversal
14:01:05.664 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:05.666 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
14:01:05.667 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
14:01:05.667 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
14:01:05.667 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:01:05.669 WARN  MafOutputRenderer - 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=
14:01:05.669 WARN  MafOutputRenderer - 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=
14:01:05.669 WARN  MafOutputRenderer - 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=
14:01:05.670 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
14:01:05.670 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:01:05.671 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:01:05.671 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:01:05.671 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:01:05.672 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
14:01:05.673 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
14:01:05.673 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
14:01:05.674 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
14:01:05.674 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
14:01:05.675 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
14:01:05.675 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
14:01:05.675 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
14:01:05.677 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:01:05.677 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
14:01:05.678 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
14:01:05.679 WARN  MafOutputRenderer - 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=
14:01:05.679 WARN  MafOutputRenderer - 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=
14:01:05.680 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:01:05.681 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
14:01:05.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
14:01:05.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:01:05.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:01:05.683 WARN  MafOutputRenderer - 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=
14:01:05.684 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:01:05.684 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:01:05.685 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:01:05.685 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
14:01:05.686 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
14:01:05.687 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:01:05.688 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
14:01:05.688 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
14:01:05.689 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
14:01:05.689 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
14:01:05.690 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
14:01:05.691 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
14:01:05.691 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
14:01:05.691 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
14:01:05.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
14:01:05.693 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
14:01:05.693 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
14:01:05.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
14:01:05.695 WARN  MafOutputRenderer - 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=
14:01:05.695 WARN  MafOutputRenderer - 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=
14:01:05.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
14:01:05.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
14:01:05.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
14:01:05.697 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
14:01:05.698 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
14:01:05.698 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
14:01:05.698 INFO  ProgressMeter -             unmapped              0.0                    57         100588.2
14:01:05.698 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:01:05.698 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:05.699 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:05.700 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12491879616010561344.vcf
14:01:05.810 INFO  Funcotator - ------------------------------------------------------------
14:01:05.810 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:05.810 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:05.810 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:05.810 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:05.810 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:05 PM GMT
14:01:05.810 INFO  Funcotator - ------------------------------------------------------------
14:01:05.810 INFO  Funcotator - ------------------------------------------------------------
14:01:05.810 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:05.810 INFO  Funcotator - Picard Version: 3.4.0
14:01:05.810 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:05.810 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:05.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:05.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:05.810 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:05.810 INFO  Funcotator - Deflater: IntelDeflater
14:01:05.810 INFO  Funcotator - Inflater: IntelInflater
14:01:05.810 INFO  Funcotator - GCS max retries/reopens: 20
14:01:05.810 INFO  Funcotator - Requester pays: disabled
14:01:05.810 INFO  Funcotator - Initializing engine
14:01:05.811 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
14:01:05.812 INFO  Funcotator - Done initializing engine
14:01:05.812 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:05.812 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:05.812 INFO  Funcotator - Initializing data sources...
14:01:05.812 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:01:05.812 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:05.812 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
14:01:05.812 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
14:01:05.812 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
14:01:05.813 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
14:01:05.813 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
14:01:05.813 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
14:01:05.813 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
14:01:05.813 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
14:01:05.813 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
14:01:05.814 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
14:01:05.814 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
14:01:05.814 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
14:01:05.814 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:05.814 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
14:01:05.814 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
14:01:05.814 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:05.814 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
14:01:05.815 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
14:01:05.834 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
14:01:05.835 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
14:01:05.880 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
14:01:05.881 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
14:01:06.470 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
14:01:06.470 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:01:06.471 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:06.473 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
14:01:06.476 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:06.478 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:01:06.478 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
14:01:06.479 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:01:06.521 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
14:01:06.521 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	2025-05-27 14:01:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:01:06.521 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
14:01:06.611 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
14:01:06.611 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
14:01:06.612 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
14:01:06.619 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:06.619 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
14:01:06.619 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:06.620 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:01:06.621 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
14:01:06.701 INFO  Funcotator - Initializing Funcotator Engine...
14:01:06.701 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:06.701 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:01:06.701 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out378641385785737456.vcf
14:01:06.702 INFO  ProgressMeter - Starting traversal
14:01:06.702 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:22.604 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7546.2
14:01:23.073 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)
14:01:23.074 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)
14:01:23.841 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7201.1
14:01:23.841 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:01:23.841 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:01:23.843 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:23 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=2866806784
14:01:23.940 INFO  Funcotator - ------------------------------------------------------------
14:01:23.940 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:23.940 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:23.940 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:23.940 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:23.941 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:23 PM GMT
14:01:23.941 INFO  Funcotator - ------------------------------------------------------------
14:01:23.941 INFO  Funcotator - ------------------------------------------------------------
14:01:23.941 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:23.941 INFO  Funcotator - Picard Version: 3.4.0
14:01:23.941 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:23.941 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:23.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:23.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:23.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:23.941 INFO  Funcotator - Deflater: IntelDeflater
14:01:23.941 INFO  Funcotator - Inflater: IntelInflater
14:01:23.941 INFO  Funcotator - GCS max retries/reopens: 20
14:01:23.941 INFO  Funcotator - Requester pays: disabled
14:01:23.941 INFO  Funcotator - Initializing engine
14:01:23.942 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
14:01:23.942 INFO  Funcotator - Done initializing engine
14:01:23.942 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:23.942 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:23.942 INFO  Funcotator - Initializing data sources...
14:01:23.942 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
14:01:23.942 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:23.942 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
14:01:23.943 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
14:01:23.943 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
14:01:23.943 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
14:01:23.943 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
14:01:23.943 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
14:01:23.943 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
14:01:23.944 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
14:01:23.944 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
14:01:23.944 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
14:01:23.944 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
14:01:23.944 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
14:01:23.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:23.945 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
14:01:23.945 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
14:01:23.945 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:23.945 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
14:01:23.945 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
14:01:23.965 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
14:01:23.966 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
14:01:24.038 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
14:01:24.038 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
14:01:24.624 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
14:01:24.624 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
14:01:24.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:24.626 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
14:01:24.629 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
14:01:24.631 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:01:24.631 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
14:01:24.632 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
14:01:24.659 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
14:01:24.659 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	2025-05-27 14:01:24	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:01:24.659 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
14:01:24.697 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
14:01:24.697 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
14:01:24.698 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
14:01:24.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
14:01:24.705 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
14:01:24.705 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:24.706 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
14:01:24.706 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
14:01:24.825 INFO  Funcotator - Initializing Funcotator Engine...
14:01:24.825 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:24.825 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:01:24.825 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14547290931419190364.maf
14:01:24.825 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
14:01:24.826 INFO  ProgressMeter - Starting traversal
14:01:24.826 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:40.688 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7565.3
14:01:41.177 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)
14:01:41.178 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)
14:01:41.959 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7203.6
14:01:41.960 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
14:01:41.960 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
14:01:41.960 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=2866806784
14:01:41.961 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out378641385785737456.vcf
14:01:42.378 INFO  Funcotator - ------------------------------------------------------------
14:01:42.378 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:42.378 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:42.378 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:42.378 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:42.378 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:42 PM GMT
14:01:42.378 INFO  Funcotator - ------------------------------------------------------------
14:01:42.378 INFO  Funcotator - ------------------------------------------------------------
14:01:42.378 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:42.378 INFO  Funcotator - Picard Version: 3.4.0
14:01:42.378 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:42.378 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:42.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:42.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:42.378 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:42.378 INFO  Funcotator - Deflater: IntelDeflater
14:01:42.378 INFO  Funcotator - Inflater: IntelInflater
14:01:42.378 INFO  Funcotator - GCS max retries/reopens: 20
14:01:42.378 INFO  Funcotator - Requester pays: disabled
14:01:42.378 INFO  Funcotator - Initializing engine
14:01:42.379 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:01:42.394 INFO  Funcotator - Done initializing engine
14:01:42.394 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:42.394 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:42.394 INFO  Funcotator - Initializing data sources...
14:01:42.394 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:42.394 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:42.394 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
14:01:42.394 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
14:01:42.394 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
14:01:42.394 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:42.394 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
14:01:42.394 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:42.395 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
14:01:42.395 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
14:01:42.396 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
14:01:42.396 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:42.396 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
14:01:42.404 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
14:01:42.412 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
14:01:42.420 INFO  Funcotator - Initializing Funcotator Engine...
14:01:42.424 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:01:42.424 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18195320020345454497.vcf
14:01:42.444 INFO  ProgressMeter - Starting traversal
14:01:42.444 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:42.466 INFO  ProgressMeter -             unmapped              0.0                   100         272727.3
14:01:42.466 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:01:42.466 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:42.471 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:42.564 INFO  Funcotator - ------------------------------------------------------------
14:01:42.564 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:42.564 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:42.564 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:42.564 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:42.564 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:42 PM GMT
14:01:42.564 INFO  Funcotator - ------------------------------------------------------------
14:01:42.564 INFO  Funcotator - ------------------------------------------------------------
14:01:42.564 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:42.564 INFO  Funcotator - Picard Version: 3.4.0
14:01:42.564 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:42.564 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:42.564 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:42.564 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:42.564 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:42.564 INFO  Funcotator - Deflater: IntelDeflater
14:01:42.564 INFO  Funcotator - Inflater: IntelInflater
14:01:42.564 INFO  Funcotator - GCS max retries/reopens: 20
14:01:42.564 INFO  Funcotator - Requester pays: disabled
14:01:42.564 INFO  Funcotator - Initializing engine
14:01:42.565 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
14:01:42.582 INFO  Funcotator - Done initializing engine
14:01:42.582 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:42.582 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:42.582 INFO  Funcotator - Initializing data sources...
14:01:42.582 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:42.582 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:42.582 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
14:01:42.582 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
14:01:42.582 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
14:01:42.582 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:42.582 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
14:01:42.582 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:42.583 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
14:01:42.583 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
14:01:42.584 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
14:01:42.584 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:42.584 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
14:01:42.592 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
14:01:42.601 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
14:01:42.608 INFO  Funcotator - Initializing Funcotator Engine...
14:01:42.613 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
14:01:42.613 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7069640282136819441.maf
14:01:42.613 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
14:01:42.614 INFO  ProgressMeter - Starting traversal
14:01:42.614 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:42.617 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.621 WARN  MafOutputRenderer - 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=
14:01:42.621 WARN  MafOutputRenderer - 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+
14:01:42.621 WARN  MafOutputRenderer - 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+
14:01:42.622 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:01:42.622 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
14:01:42.622 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.622 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.623 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.623 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.623 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.623 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.624 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.624 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.624 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.624 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.625 WARN  MafOutputRenderer - 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=
14:01:42.625 WARN  MafOutputRenderer - 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=
14:01:42.625 WARN  MafOutputRenderer - 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=
14:01:42.625 WARN  MafOutputRenderer - 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+
14:01:42.626 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
14:01:42.626 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.626 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:42.627 WARN  MafOutputRenderer - 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=
14:01:42.627 WARN  MafOutputRenderer - 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=
14:01:42.627 WARN  MafOutputRenderer - 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=
14:01:42.627 WARN  MafOutputRenderer - 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=
14:01:42.627 WARN  MafOutputRenderer - 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=
14:01:42.628 WARN  MafOutputRenderer - 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
14:01:42.628 WARN  MafOutputRenderer - 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=
14:01:42.628 WARN  MafOutputRenderer - 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=
14:01:42.629 WARN  MafOutputRenderer - 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=
14:01:42.629 WARN  MafOutputRenderer - 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=
14:01:42.629 WARN  MafOutputRenderer - 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=
14:01:42.629 WARN  MafOutputRenderer - 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=
14:01:42.629 WARN  MafOutputRenderer - 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=
14:01:42.630 WARN  MafOutputRenderer - 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=
14:01:42.630 WARN  MafOutputRenderer - 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=
14:01:42.630 WARN  MafOutputRenderer - 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=
14:01:42.630 WARN  MafOutputRenderer - 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=
14:01:42.630 WARN  MafOutputRenderer - 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=
14:01:42.632 WARN  MafOutputRenderer - 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=
14:01:42.632 WARN  MafOutputRenderer - 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=
14:01:42.632 WARN  MafOutputRenderer - 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=
14:01:42.632 WARN  MafOutputRenderer - 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=
14:01:42.632 WARN  MafOutputRenderer - 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=
14:01:42.633 WARN  MafOutputRenderer - 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+
14:01:42.633 WARN  MafOutputRenderer - 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=
14:01:42.633 WARN  MafOutputRenderer - 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=
14:01:42.633 WARN  MafOutputRenderer - 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=
14:01:42.633 WARN  MafOutputRenderer - 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=
14:01:42.633 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.634 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.635 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.636 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.637 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.638 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.639 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.640 WARN  MafOutputRenderer - 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=
14:01:42.641 WARN  MafOutputRenderer - 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=
14:01:42.641 WARN  MafOutputRenderer - 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=
14:01:42.641 WARN  MafOutputRenderer - 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=
14:01:42.641 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
14:01:42.641 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
14:01:42.641 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:42.641 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:42.642 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out18195320020345454497.vcf
14:01:42.798 INFO  Funcotator - ------------------------------------------------------------
14:01:42.798 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:42.798 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:42.798 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:42.798 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:42.798 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:42 PM GMT
14:01:42.798 INFO  Funcotator - ------------------------------------------------------------
14:01:42.798 INFO  Funcotator - ------------------------------------------------------------
14:01:42.798 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:42.798 INFO  Funcotator - Picard Version: 3.4.0
14:01:42.798 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:42.798 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:42.798 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:42.798 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:42.798 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:42.798 INFO  Funcotator - Deflater: IntelDeflater
14:01:42.798 INFO  Funcotator - Inflater: IntelInflater
14:01:42.798 INFO  Funcotator - GCS max retries/reopens: 20
14:01:42.798 INFO  Funcotator - Requester pays: disabled
14:01:42.798 INFO  Funcotator - Initializing engine
14:01:42.799 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:01:42.800 INFO  Funcotator - Done initializing engine
14:01:42.800 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:42.800 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:42.800 INFO  Funcotator - Initializing data sources...
14:01:42.800 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:42.800 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:42.800 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
14:01:42.800 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
14:01:42.800 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
14:01:42.800 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:42.800 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
14:01:42.800 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:42.801 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
14:01:42.801 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
14:01:42.801 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
14:01:42.801 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:42.802 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
14:01:42.803 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
14:01:42.804 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
14:01:42.804 INFO  Funcotator - Initializing Funcotator Engine...
14:01:42.804 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:42.804 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.
14:01:42.804 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:42.804 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11363473430336751444.vcf
14:01:42.805 INFO  ProgressMeter - Starting traversal
14:01:42.805 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:42.834 INFO  ProgressMeter -             unmapped              0.0                    57         117931.0
14:01:42.835 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:01:42.835 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:42.837 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:42.930 INFO  Funcotator - ------------------------------------------------------------
14:01:42.930 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:42.930 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:42.930 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:42.930 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:42.930 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:42 PM GMT
14:01:42.930 INFO  Funcotator - ------------------------------------------------------------
14:01:42.930 INFO  Funcotator - ------------------------------------------------------------
14:01:42.930 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:42.930 INFO  Funcotator - Picard Version: 3.4.0
14:01:42.930 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:42.930 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:42.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:42.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:42.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:42.930 INFO  Funcotator - Deflater: IntelDeflater
14:01:42.930 INFO  Funcotator - Inflater: IntelInflater
14:01:42.930 INFO  Funcotator - GCS max retries/reopens: 20
14:01:42.930 INFO  Funcotator - Requester pays: disabled
14:01:42.930 INFO  Funcotator - Initializing engine
14:01:42.931 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
14:01:42.931 INFO  Funcotator - Done initializing engine
14:01:42.931 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:42.931 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:42.931 INFO  Funcotator - Initializing data sources...
14:01:42.931 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:42.931 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:42.932 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
14:01:42.932 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
14:01:42.932 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
14:01:42.932 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:42.932 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
14:01:42.932 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:42.933 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
14:01:42.933 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
14:01:42.933 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
14:01:42.933 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:42.934 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
14:01:42.934 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
14:01:42.935 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
14:01:42.936 INFO  Funcotator - Initializing Funcotator Engine...
14:01:42.936 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:42.936 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.
14:01:42.936 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
14:01:42.936 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15730161434172569675.maf
14:01:42.936 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
14:01:42.936 INFO  ProgressMeter - Starting traversal
14:01:42.937 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:42.939 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
14:01:42.939 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
14:01:42.939 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 @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
14:01:42.940 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 @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:01:42.941 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
14:01:42.941 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
14:01:42.942 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 @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:01:42.942 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 @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
14:01:42.943 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 @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:01:42.943 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 @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
14:01:42.944 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:01:42.944 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 @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
14:01:42.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
14:01:42.947 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 @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
14:01:42.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
14:01:42.948 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 @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
14:01:42.949 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 @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
14:01:42.949 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 @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
14:01:42.950 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 @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
14:01:42.950 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 @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
14:01:42.952 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 @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:01:42.952 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
14:01:42.954 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
14:01:42.955 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
14:01:42.955 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
14:01:42.957 WARN  MafOutputRenderer - 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=
14:01:42.958 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
14:01:42.960 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
14:01:42.960 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
14:01:42.961 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
14:01:42.961 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
14:01:42.962 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
14:01:42.963 WARN  MafOutputRenderer - 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=
14:01:42.963 WARN  MafOutputRenderer - 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=
14:01:42.963 WARN  MafOutputRenderer - 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=
14:01:42.965 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
14:01:42.965 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
14:01:42.966 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
14:01:42.967 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
14:01:42.967 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
14:01:42.967 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
14:01:42.969 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
14:01:42.969 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
14:01:42.969 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
14:01:42.970 WARN  MafOutputRenderer - 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=
14:01:42.971 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
14:01:42.971 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
14:01:42.971 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
14:01:42.972 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
14:01:42.973 WARN  MafOutputRenderer - 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=
14:01:42.973 WARN  MafOutputRenderer - 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=
14:01:42.974 WARN  MafOutputRenderer - 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=
14:01:42.974 WARN  MafOutputRenderer - 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=
14:01:42.975 WARN  MafOutputRenderer - 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=
14:01:42.976 WARN  MafOutputRenderer - 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=
14:01:42.976 WARN  MafOutputRenderer - 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=
14:01:42.976 WARN  MafOutputRenderer - 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=
14:01:42.976 INFO  ProgressMeter -             unmapped              0.0                    57          87692.3
14:01:42.976 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
14:01:42.976 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
14:01:42.977 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:42.978 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11363473430336751444.vcf
14:01:43.104 INFO  Funcotator - ------------------------------------------------------------
14:01:43.104 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:43.104 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:43.104 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:43.104 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:43.104 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:43 PM GMT
14:01:43.104 INFO  Funcotator - ------------------------------------------------------------
14:01:43.104 INFO  Funcotator - ------------------------------------------------------------
14:01:43.104 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:43.104 INFO  Funcotator - Picard Version: 3.4.0
14:01:43.104 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:43.104 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:43.104 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:43.104 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:43.104 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:43.104 INFO  Funcotator - Deflater: IntelDeflater
14:01:43.104 INFO  Funcotator - Inflater: IntelInflater
14:01:43.104 INFO  Funcotator - GCS max retries/reopens: 20
14:01:43.104 INFO  Funcotator - Requester pays: disabled
14:01:43.104 INFO  Funcotator - Initializing engine
14:01:43.105 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
14:01:43.106 INFO  Funcotator - Done initializing engine
14:01:43.106 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:43.106 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:43.106 INFO  Funcotator - Initializing data sources...
14:01:43.106 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
14:01:43.106 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:43.106 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
14:01:43.106 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
14:01:43.107 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
14:01:43.107 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:43.107 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
14:01:43.107 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:43.107 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
14:01:43.108 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
14:01:43.108 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
14:01:43.108 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
14:01:43.108 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
14:01:43.109 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
14:01:43.110 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
14:01:43.111 INFO  Funcotator - Initializing Funcotator Engine...
14:01:43.111 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:43.111 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.
14:01:43.111 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8729197475320672982.maf
14:01:43.112 INFO  ProgressMeter - Starting traversal
14:01:43.112 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:43.114 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178872355 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=
14:01:43.115 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.116 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.116 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.117 WARN  MafOutputRenderer - 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=
14:01:43.117 WARN  MafOutputRenderer - 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=
14:01:43.117 WARN  MafOutputRenderer - 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=
14:01:43.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.119 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.119 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.119 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.119 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.120 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.120 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.120 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
14:01:43.122 WARN  MafOutputRenderer - 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=
14:01:43.122 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
14:01:43.122 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:01:43.122 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
14:01:43.122 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:43.222 INFO  Funcotator - ------------------------------------------------------------
14:01:43.222 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:43.222 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:43.222 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:43.222 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:43.222 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:43 PM GMT
14:01:43.222 INFO  Funcotator - ------------------------------------------------------------
14:01:43.222 INFO  Funcotator - ------------------------------------------------------------
14:01:43.222 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:43.222 INFO  Funcotator - Picard Version: 3.4.0
14:01:43.222 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:43.222 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:43.222 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:43.222 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:43.222 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:43.222 INFO  Funcotator - Deflater: IntelDeflater
14:01:43.222 INFO  Funcotator - Inflater: IntelInflater
14:01:43.222 INFO  Funcotator - GCS max retries/reopens: 20
14:01:43.222 INFO  Funcotator - Requester pays: disabled
14:01:43.222 INFO  Funcotator - Initializing engine
14:01:43.223 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
14:01:43.224 INFO  Funcotator - Done initializing engine
14:01:43.224 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:43.224 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:43.224 INFO  Funcotator - Initializing data sources...
14:01:43.224 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:01:43.224 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:43.224 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
14:01:43.225 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
14:01:43.225 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
14:01:43.225 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:43.225 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:01:43.225 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
14:01:43.226 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
14:01:43.253 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
14:01:43.253 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	2025-05-27 14:01:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:01:43.253 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
14:01:43.254 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:43.254 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
14:01:43.255 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
14:01:43.255 INFO  Funcotator - Initializing Funcotator Engine...
14:01:43.256 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:43.256 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.
14:01:43.256 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out236049210417564051.vcf
14:01:43.259 INFO  ProgressMeter - Starting traversal
14:01:43.259 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:43.263 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
14:01:43.263 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
14:01:43.263 WARN  Funcotator - ================================================================================
14:01:43.263 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:01:43.263 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:01:43.263 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:01:43.263 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:01:43.263 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:01:43.263 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:01:43.263 WARN  Funcotator - --------------------------------------------------------------------------------
14:01:43.263 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:01:43.263 WARN  Funcotator -  run was misconfigured.     
14:01:43.263 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:01:43.263 WARN  Funcotator - ================================================================================
14:01:43.263 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:43.264 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out236049210417564051.vcf
14:01:43.359 INFO  Funcotator - ------------------------------------------------------------
14:01:43.359 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:01:43.359 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:01:43.359 INFO  Funcotator - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:01:43.359 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:01:43.359 INFO  Funcotator - Start Date/Time: May 27, 2025 at 2:01:43 PM GMT
14:01:43.359 INFO  Funcotator - ------------------------------------------------------------
14:01:43.359 INFO  Funcotator - ------------------------------------------------------------
14:01:43.359 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:01:43.359 INFO  Funcotator - Picard Version: 3.4.0
14:01:43.359 INFO  Funcotator - Built for Spark Version: 3.5.0
14:01:43.359 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:01:43.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:01:43.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:01:43.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:01:43.359 INFO  Funcotator - Deflater: IntelDeflater
14:01:43.359 INFO  Funcotator - Inflater: IntelInflater
14:01:43.359 INFO  Funcotator - GCS max retries/reopens: 20
14:01:43.359 INFO  Funcotator - Requester pays: disabled
14:01:43.359 INFO  Funcotator - Initializing engine
14:01:43.360 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
14:01:43.361 INFO  Funcotator - Done initializing engine
14:01:43.361 INFO  Funcotator - Skipping sequence dictionary validation.
14:01:43.361 INFO  Funcotator - Processing user transcripts/defaults/overrides...
14:01:43.361 INFO  Funcotator - Initializing data sources...
14:01:43.361 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
14:01:43.361 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
14:01:43.361 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
14:01:43.362 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
14:01:43.362 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
14:01:43.362 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
14:01:43.362 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
14:01:43.362 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
14:01:43.362 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
14:01:43.390 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
14:01:43.390 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	2025-05-27 14:01:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
14:01:43.390 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
14:01:43.390 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
14:01:43.391 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
14:01:43.391 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
14:01:43.392 INFO  Funcotator - Initializing Funcotator Engine...
14:01:43.392 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
14:01:43.392 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.
14:01:43.392 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6903217315828574603.vcf
14:01:43.395 INFO  ProgressMeter - Starting traversal
14:01:43.395 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:01:43.397 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
14:01:43.397 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
14:01:43.397 WARN  Funcotator - ================================================================================
14:01:43.397 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
14:01:43.397 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
14:01:43.397 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
14:01:43.397 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
14:01:43.397 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
14:01:43.397 WARN  Funcotator -                                                   |___/                         ?[0;0m
14:01:43.397 WARN  Funcotator - --------------------------------------------------------------------------------
14:01:43.397 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
14:01:43.397 WARN  Funcotator -  run was misconfigured.     
14:01:43.397 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
14:01:43.397 WARN  Funcotator - ================================================================================
14:01:43.397 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 2:01:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2866806784
14:01:43.398 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6903217315828574603.vcf